hs-samtools 0.9.0.0 → 0.10.0.0

raw patch · 133 files changed

+12491/−2946 lines, 133 filesdep +arraydep +base16dep +binarydep ~basedep ~bitvecdep ~bytestringPVP ok

version bump matches the API change (PVP)

Dependencies added: array, base16, binary, deepseq, digest, mason, parsers, zlib

Dependency ranges changed: base, bitvec, bytestring, crypton, streamly, streamly-bytestring, streamly-core

API changes (from Hackage documentation)

Files

• CHANGELOG.md +14/−0
• LICENSE +1/−1
• hs-samtools.cabal +91/−30
• src/Data/BAM/Version1_6/BAM.hs +63/−0
• src/Data/BAM/Version1_6/BAM/Alignment.hs +38/−0
• src/Data/BAM/Version1_6/BAM/Alignment/Base.hs +176/−0
• src/Data/BAM/Version1_6/BAM/Alignment/OptionalFields/AOPT.hs +72/−0
• src/Data/BAM/Version1_6/BAM/Alignment/OptionalFields/BOPT.hs +416/−0
• src/Data/BAM/Version1_6/BAM/Alignment/OptionalFields/Base.hs +158/−0
• src/Data/BAM/Version1_6/BAM/Alignment/OptionalFields/BigCOPT.hs +71/−0
• src/Data/BAM/Version1_6/BAM/Alignment/OptionalFields/BigIOPT.hs +71/−0
• src/Data/BAM/Version1_6/BAM/Alignment/OptionalFields/BigSOPT.hs +71/−0
• src/Data/BAM/Version1_6/BAM/Alignment/OptionalFields/FOPT.hs +71/−0
• src/Data/BAM/Version1_6/BAM/Alignment/OptionalFields/HOPT.hs +71/−0
• src/Data/BAM/Version1_6/BAM/Alignment/OptionalFields/SmallCOPT.hs +71/−0
• src/Data/BAM/Version1_6/BAM/Alignment/OptionalFields/SmallIOPT.hs +71/−0
• src/Data/BAM/Version1_6/BAM/Alignment/OptionalFields/SmallSOPT.hs +71/−0
• src/Data/BAM/Version1_6/BAM/Alignment/OptionalFields/ZOPT.hs +72/−0
• src/Data/BAM/Version1_6/BAM/BAMAlignments.hs +49/−0
• src/Data/BAM/Version1_6/BAM/BAMHeader.hs +81/−0
• src/Data/BAM/Version1_6/BAM/Header.hs +46/−0
• src/Data/BAM/Version1_6/BAM/Header/CO.hs +45/−0
• src/Data/BAM/Version1_6/BAM/Header/HD.hs +137/−0
• src/Data/BAM/Version1_6/BAM/Header/PG.hs +185/−0
• src/Data/BAM/Version1_6/BAM/Header/RG.hs +391/−0
• src/Data/BAM/Version1_6/BAM/Header/SQ.hs +291/−0
• src/Data/BAM/Version1_6/BAM/ReferenceInformation.hs +38/−0
• src/Data/BAM/Version1_6/BAM/ReferenceInformation/Base.hs +62/−0
• src/Data/BAM/Version1_6/BGZFBlock.hs +112/−0
• src/Data/BAM/Version1_6/Base.hs +51/−0
• src/Data/BAM/Version1_6/GZipHeader.hs +98/−0
• src/Data/BAM/Version1_6/Internal.hs +335/−0
• src/Data/BAM/Version1_6/Read/Base.hs +113/−0
• src/Data/BAM/Version1_6/Read/Error.hs +319/−0
• src/Data/BAM/Version1_6/Read/Parser/BAM/Alignment/Base.hs +1117/−0
• src/Data/BAM/Version1_6/Read/Parser/BAM/Alignment/Internal.hs +79/−0
• src/Data/BAM/Version1_6/Read/Parser/BAM/Alignment/OptionalFields/AOPT.hs +92/−0
• src/Data/BAM/Version1_6/Read/Parser/BAM/Alignment/OptionalFields/BOPT.hs +343/−0
• src/Data/BAM/Version1_6/Read/Parser/BAM/Alignment/OptionalFields/BigCOPT.hs +84/−0
• src/Data/BAM/Version1_6/Read/Parser/BAM/Alignment/OptionalFields/BigIOPT.hs +84/−0
• src/Data/BAM/Version1_6/Read/Parser/BAM/Alignment/OptionalFields/BigSOPT.hs +84/−0
• src/Data/BAM/Version1_6/Read/Parser/BAM/Alignment/OptionalFields/FOPT.hs +95/−0
• src/Data/BAM/Version1_6/Read/Parser/BAM/Alignment/OptionalFields/HOPT.hs +110/−0
• src/Data/BAM/Version1_6/Read/Parser/BAM/Alignment/OptionalFields/SmallCOPT.hs +84/−0
• src/Data/BAM/Version1_6/Read/Parser/BAM/Alignment/OptionalFields/SmallIOPT.hs +84/−0
• src/Data/BAM/Version1_6/Read/Parser/BAM/Alignment/OptionalFields/SmallSOPT.hs +84/−0
• src/Data/BAM/Version1_6/Read/Parser/BAM/Alignment/OptionalFields/ZOPT.hs +97/−0
• src/Data/BAM/Version1_6/Read/Parser/BAM/BAMAlignments.hs +34/−0
• src/Data/BAM/Version1_6/Read/Parser/BAM/BAMHeader.hs +72/−0
• src/Data/BAM/Version1_6/Read/Parser/BAM/Base.hs +57/−0
• src/Data/BAM/Version1_6/Read/Parser/BAM/ReferenceInformation/Base.hs +66/−0
• src/Data/BAM/Version1_6/Read/Parser/BGZFBlock.hs +268/−0
• src/Data/BAM/Version1_6/Write/Base.hs +1082/−0
• src/Data/BAM/Version1_6/Write/Error.hs +33/−0
• src/Data/BAM/Version1_6/Write/Internal.hs +68/−0
• src/Data/SAM/Version1_6/Alignment.hs +1/−1
• src/Data/SAM/Version1_6/Alignment/AOPT.hs +0/−68
• src/Data/SAM/Version1_6/Alignment/BOPT.hs +0/−294
• src/Data/SAM/Version1_6/Alignment/Base.hs +134/−153
• src/Data/SAM/Version1_6/Alignment/FOPT.hs +0/−68
• src/Data/SAM/Version1_6/Alignment/HOPT.hs +0/−68
• src/Data/SAM/Version1_6/Alignment/IOPT.hs +0/−68
• src/Data/SAM/Version1_6/Alignment/OptionalFields/AOPT.hs +70/−0
• src/Data/SAM/Version1_6/Alignment/OptionalFields/BOPT.hs +352/−0
• src/Data/SAM/Version1_6/Alignment/OptionalFields/Base.hs +89/−0
• src/Data/SAM/Version1_6/Alignment/OptionalFields/FOPT.hs +70/−0
• src/Data/SAM/Version1_6/Alignment/OptionalFields/HOPT.hs +70/−0
• src/Data/SAM/Version1_6/Alignment/OptionalFields/IOPT.hs +70/−0
• src/Data/SAM/Version1_6/Alignment/OptionalFields/ZOPT.hs +70/−0
• src/Data/SAM/Version1_6/Alignment/ZOPT.hs +0/−68
• src/Data/SAM/Version1_6/Header.hs +1/−1
• src/Data/SAM/Version1_6/Header/CO.hs +8/−5
• src/Data/SAM/Version1_6/Header/HD.hs +41/−30
• src/Data/SAM/Version1_6/Header/PG.hs +59/−44
• src/Data/SAM/Version1_6/Header/RG.hs +131/−100
• src/Data/SAM/Version1_6/Header/SQ.hs +95/−72
• src/Data/SAM/Version1_6/Internal.hs +27/−0
• src/Data/SAM/Version1_6/Read/Base.hs +102/−72
• src/Data/SAM/Version1_6/Read/Error.hs +9/−1
• src/Data/SAM/Version1_6/Read/Parser/Alignment/AOPT.hs +0/−80
• src/Data/SAM/Version1_6/Read/Parser/Alignment/BOPT.hs +0/−173
• src/Data/SAM/Version1_6/Read/Parser/Alignment/Base.hs +493/−164
• src/Data/SAM/Version1_6/Read/Parser/Alignment/FOPT.hs +0/−83
• src/Data/SAM/Version1_6/Read/Parser/Alignment/HOPT.hs +0/−80
• src/Data/SAM/Version1_6/Read/Parser/Alignment/IOPT.hs +0/−83
• src/Data/SAM/Version1_6/Read/Parser/Alignment/OptionalFields/AOPT.hs +94/−0
• src/Data/SAM/Version1_6/Read/Parser/Alignment/OptionalFields/BOPT.hs +216/−0
• src/Data/SAM/Version1_6/Read/Parser/Alignment/OptionalFields/FOPT.hs +97/−0
• src/Data/SAM/Version1_6/Read/Parser/Alignment/OptionalFields/HOPT.hs +94/−0
• src/Data/SAM/Version1_6/Read/Parser/Alignment/OptionalFields/IOPT.hs +97/−0
• src/Data/SAM/Version1_6/Read/Parser/Alignment/OptionalFields/ZOPT.hs +94/−0
• src/Data/SAM/Version1_6/Read/Parser/Alignment/ZOPT.hs +0/−80
• src/Data/SAM/Version1_6/Read/Parser/Header/CO/Base.hs +17/−10
• src/Data/SAM/Version1_6/Read/Parser/Header/HD/Base.hs +25/−18
• src/Data/SAM/Version1_6/Read/Parser/Header/HD/GO.hs +22/−14
• src/Data/SAM/Version1_6/Read/Parser/Header/HD/SO.hs +22/−14
• src/Data/SAM/Version1_6/Read/Parser/Header/HD/SS.hs +23/−14
• src/Data/SAM/Version1_6/Read/Parser/Header/HD/VN.hs +23/−14
• src/Data/SAM/Version1_6/Read/Parser/Header/PG/Base.hs +29/−22
• src/Data/SAM/Version1_6/Read/Parser/Header/PG/CL.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/PG/DS.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/PG/ID.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/PG/PN.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/PG/PP.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/PG/VN.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/RG/BC.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/RG/Base.hs +45/−38
• src/Data/SAM/Version1_6/Read/Parser/Header/RG/CN.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/RG/DS.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/RG/DT.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/RG/FO.hs +23/−14
• src/Data/SAM/Version1_6/Read/Parser/Header/RG/ID.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/RG/KS.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/RG/LB.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/RG/PG.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/RG/PI.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/RG/PL.hs +23/−14
• src/Data/SAM/Version1_6/Read/Parser/Header/RG/PM.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/RG/PU.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/RG/SM.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AH.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AN.hs +23/−14
• src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AS.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/SQ/Base.hs +36/−29
• src/Data/SAM/Version1_6/Read/Parser/Header/SQ/DS.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/SQ/LN.hs +23/−14
• src/Data/SAM/Version1_6/Read/Parser/Header/SQ/M5.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/SQ/SN.hs +23/−14
• src/Data/SAM/Version1_6/Read/Parser/Header/SQ/SP.hs +15/−9
• src/Data/SAM/Version1_6/Read/Parser/Header/SQ/TP.hs +23/−14
• src/Data/SAM/Version1_6/Read/Parser/Header/SQ/UR.hs +15/−9
• src/Data/SAM/Version1_6/Write/Base.hs +988/−531
• test/Main.hs +40/−55

@@ -93,3 +93,17 @@  * Fixed BOPT deconstruction in deconstructSAM_V1_6 (writeSAM_V1_6). * Added extra writeSAM_V1_6 test cases.++## 0.9.0.0 -- 2023-10-31++* Fixed writeSAM_V1_6 function.+* Added additional test cases for writeSAM_V1_6.++## 0.10.0.0 -- 2024-07-15++* Fixed SAM parsing of optional fields.+* Reorganized/refactored SAM modules.+* Added BAM parsing.+* Added internal modules.+* Updated copyright in all modules.+* Updated LICENSE with updated year.

@@ -1,4 +1,4 @@-Copyright (c) 2023, Matthew Mosior+Copyright (c) 2024, Matthew Mosior  All rights reserved. 

@@ -20,7 +20,7 @@ -- PVP summary:     +-+------- breaking API changes --                  | | +----- non-breaking API additions --                  | | | +--- code changes with no API change-version:            0.9.0.0+version:            0.10.0.0  -- A short (one-line) description of the package. synopsis: Read and write SAM, BAM, and CRAM files.@@ -65,15 +65,65 @@     import:           warnings      -- Modules exported by the library.-    exposed-modules: Data.SAM.Version1_6.Base,+    exposed-modules: Data.BAM.Version1_6.Base,+                     Data.BAM.Version1_6.BAM,+                     Data.BAM.Version1_6.BAM.BAMAlignments,+                     Data.BAM.Version1_6.BAM.BAMHeader,+                     Data.BAM.Version1_6.BAM.Alignment,+                     Data.BAM.Version1_6.BAM.Alignment.Base,+                     Data.BAM.Version1_6.BAM.Alignment.OptionalFields.Base,+                     Data.BAM.Version1_6.BAM.Alignment.OptionalFields.AOPT,+                     Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BigCOPT,+                     Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BigIOPT,+                     Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BigSOPT,+                     Data.BAM.Version1_6.BAM.Alignment.OptionalFields.SmallCOPT,+                     Data.BAM.Version1_6.BAM.Alignment.OptionalFields.SmallIOPT,+                     Data.BAM.Version1_6.BAM.Alignment.OptionalFields.SmallSOPT,+                     Data.BAM.Version1_6.BAM.Alignment.OptionalFields.FOPT,+                     Data.BAM.Version1_6.BAM.Alignment.OptionalFields.HOPT,+                     Data.BAM.Version1_6.BAM.Alignment.OptionalFields.ZOPT,+                     Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BOPT,+                     Data.BAM.Version1_6.BAM.Header, +                     Data.BAM.Version1_6.BAM.Header.CO,+                     Data.BAM.Version1_6.BAM.Header.HD,+                     Data.BAM.Version1_6.BAM.Header.PG,+                     Data.BAM.Version1_6.BAM.Header.RG,+                     Data.BAM.Version1_6.BAM.Header.SQ, +                     Data.BAM.Version1_6.BAM.ReferenceInformation,+                     Data.BAM.Version1_6.BAM.ReferenceInformation.Base,+                     Data.BAM.Version1_6.BGZFBlock,+                     Data.BAM.Version1_6.GZipHeader,+                     Data.BAM.Version1_6.Read.Base,+                     Data.BAM.Version1_6.Read.Error,+                     Data.BAM.Version1_6.Read.Parser.BGZFBlock,+                     Data.BAM.Version1_6.Read.Parser.BAM.Base,+                     Data.BAM.Version1_6.Read.Parser.BAM.BAMAlignments,+                     Data.BAM.Version1_6.Read.Parser.BAM.BAMHeader,+                     Data.BAM.Version1_6.Read.Parser.BAM.Alignment.Base,+                     Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.AOPT,+                     Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BigCOPT,+                     Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BigIOPT,+                     Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BigSOPT,+                     Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.SmallCOPT,+                     Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.SmallIOPT,+                     Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.SmallSOPT,+                     Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.FOPT,+                     Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.HOPT,+                     Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.ZOPT,+                     Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BOPT,+                     Data.BAM.Version1_6.Read.Parser.BAM.ReferenceInformation.Base,+                     Data.BAM.Version1_6.Write.Base,+                     Data.BAM.Version1_6.Write.Error,+                     Data.SAM.Version1_6.Base,                      Data.SAM.Version1_6.Alignment,                      Data.SAM.Version1_6.Alignment.Base,-                     Data.SAM.Version1_6.Alignment.AOPT,-                     Data.SAM.Version1_6.Alignment.FOPT,-                     Data.SAM.Version1_6.Alignment.HOPT,-                     Data.SAM.Version1_6.Alignment.IOPT,-                     Data.SAM.Version1_6.Alignment.ZOPT,-                     Data.SAM.Version1_6.Alignment.BOPT,+                     Data.SAM.Version1_6.Alignment.OptionalFields.Base,+                     Data.SAM.Version1_6.Alignment.OptionalFields.AOPT,+                     Data.SAM.Version1_6.Alignment.OptionalFields.FOPT,+                     Data.SAM.Version1_6.Alignment.OptionalFields.HOPT,+                     Data.SAM.Version1_6.Alignment.OptionalFields.IOPT,+                     Data.SAM.Version1_6.Alignment.OptionalFields.ZOPT,+                     Data.SAM.Version1_6.Alignment.OptionalFields.BOPT,                      Data.SAM.Version1_6.Header,                       Data.SAM.Version1_6.Header.CO,                      Data.SAM.Version1_6.Header.HD,@@ -83,12 +133,12 @@                      Data.SAM.Version1_6.Read.Base,                      Data.SAM.Version1_6.Read.Error,                      Data.SAM.Version1_6.Read.Parser.Alignment.Base,-                     Data.SAM.Version1_6.Read.Parser.Alignment.AOPT,-                     Data.SAM.Version1_6.Read.Parser.Alignment.IOPT,-                     Data.SAM.Version1_6.Read.Parser.Alignment.FOPT,-                     Data.SAM.Version1_6.Read.Parser.Alignment.ZOPT,-                     Data.SAM.Version1_6.Read.Parser.Alignment.HOPT,-                     Data.SAM.Version1_6.Read.Parser.Alignment.BOPT,+                     Data.SAM.Version1_6.Read.Parser.Alignment.OptionalFields.AOPT,+                     Data.SAM.Version1_6.Read.Parser.Alignment.OptionalFields.IOPT,+                     Data.SAM.Version1_6.Read.Parser.Alignment.OptionalFields.FOPT,+                     Data.SAM.Version1_6.Read.Parser.Alignment.OptionalFields.ZOPT,+                     Data.SAM.Version1_6.Read.Parser.Alignment.OptionalFields.HOPT,+                     Data.SAM.Version1_6.Read.Parser.Alignment.OptionalFields.BOPT,                      Data.SAM.Version1_6.Read.Parser.Header.HD.Base,                      Data.SAM.Version1_6.Read.Parser.Header.HD.VN,                      Data.SAM.Version1_6.Read.Parser.Header.HD.SO,@@ -131,26 +181,37 @@                      Data.SAM.Version1_6.Write.Base      -- Modules included in this library but not exported.-    -- other-modules:+    other-modules: Data.BAM.Version1_6.Internal,+                   Data.BAM.Version1_6.Read.Parser.BAM.Alignment.Internal,+                   Data.BAM.Version1_6.Write.Internal,+                   Data.SAM.Version1_6.Internal      -- LANGUAGE extensions used by modules in this package.     -- other-extensions:      -- Other library packages from which modules are imported.-    build-depends:    base                 ^>=4.17.1.0, -                      ascii                >= 1.7.0 && < 1.8,-                      attoparsec           >= 0.14.4 && < 0.15,-                      bitvec               >= 1.1.4 && < 1.2,-                      bytestring           >= 0.11.4 && < 0.12,-                      containers           >= 0.6.7 && < 0.7,-                      crypton              >= 0.33 && < 0.34,-                      generic-deriving     >= 1.14.5 && < 1.15,-                      parser-combinators   >= 1.3.0 && < 1.4,-                      pcre-heavy           >= 1.0.0 && < 1.1,-                      regex-tdfa           >= 1.3.2 && < 1.4,-                      streamly             >= 0.9.0 && < 0.10,-                      streamly-bytestring  >= 0.2.0 && < 0.3,-                      streamly-core        >= 0.1.0 && < 0.2 +    build-depends: base                >= 4.18.2 && < 4.19,+                   array               >= 0.5.6 && < 0.6,+                   ascii               >= 1.7.0 && < 1.8,+                   base16              >= 1.0 && < 1.1,+                   binary              >= 0.8.9 && < 0.9,+                   bytestring          >= 0.11.5 && < 0.12,+                   containers          >= 0.6.7 && < 0.7,+                   attoparsec          >= 0.14.4 && < 0.15,+                   bitvec              >= 1.1.5 && < 1.2,+                   crypton             >= 1.0.0 && < 1.1,+                   deepseq             >= 1.4.8 && < 1.5,+                   digest              >= 0.0.2 && < 0.1,+                   generic-deriving    >= 1.14.5 && < 1.15,+                   mason               >= 0.2.6 && < 0.3,+                   parsers             >= 0.12.11 && < 0.13,+                   parser-combinators  >= 1.3.0 && < 1.4,+                   pcre-heavy          >= 1.0.0 && < 1.1,+                   regex-tdfa          >= 1.3.2 && < 1.4,+                   streamly            >= 0.10.0 && < 0.11,+                   streamly-bytestring >= 0.2.1 && < 0.3,+                   streamly-core       >= 0.2.1 && < 0.3,+                   zlib                >= 0.7.1 && < 0.8      -- Directories containing source files.     hs-source-dirs:   src@@ -181,7 +242,7 @@     main-is:          Main.hs      -- Test dependencies.-    build-depends: base ^>=4.17.1.0,+    build-depends: base,                    bytestring,                    containers,                    hspec,

@@ -0,0 +1,63 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM ( -- * BAM_V1_6_BAM version 1.6 data type+                                 BAM_V1_6_BAM(..)+                               ) where++import Data.BAM.Version1_6.BAM.BAMHeader+import Data.BAM.Version1_6.BAM.BAMAlignments++import Data.Data+import Generics.Deriving.Base++-- | Custom @"BAM_V1_6_BAM"@ (BAM version 1.6) data type.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM = BAM_V1_6_BAM+  { bam_v1_6_bam_bamheader          :: Maybe BAM_V1_6_BAM_BAMHeader+  , bam_v1_6_bam_bamalignments      :: Maybe BAM_V1_6_BAM_BAMAlignments+  , bam_v1_6_bam_endoffilemarker    :: Bool+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM where+  BAM_V1_6_BAM bam_v1_6_bam_bamheader1+               bam_v1_6_bam_bamalignments1+               bam_v1_6_bam_endoffilemarker1 ==+    BAM_V1_6_BAM bam_v1_6_bam_bamheader2+                 bam_v1_6_bam_bamalignments2+                 bam_v1_6_bam_endoffilemarker2 =+      bam_v1_6_bam_bamheader1          == bam_v1_6_bam_bamheader2     &&+      bam_v1_6_bam_bamalignments1      == bam_v1_6_bam_bamalignments2 &&+      bam_v1_6_bam_endoffilemarker1    == bam_v1_6_bam_endoffilemarker2++instance Show BAM_V1_6_BAM where+  show (BAM_V1_6_BAM header+                     alignments+                     endoffilemarker+       ) =+    "BAM_V1_6_BAM { "                       +++    "bam_v1_6_bam_bamheader = "             +++    (show header)                           +++    " , bam_v1_6_bam_alignments = "         +++    (show alignments)                       +++    " , bam_v1_6_bam_endoffilemarker = "    +++    (show endoffilemarker)                  +++    " }"

@@ -0,0 +1,38 @@+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Alignment+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Alignment ( -- * BAM version 1.6 alignment mandatory and optional data types (RE-EXPORT)+                                           module Data.BAM.Version1_6.BAM.Alignment.Base+                                         ) where++-- | Re-exports.+import Data.BAM.Version1_6.BAM.Alignment.Base

@@ -0,0 +1,176 @@+{-# LANGUAGE DeriveDataTypeable          #-}+{-# LANGUAGE DeriveGeneric               #-}+{-# LANGUAGE FlexibleContexts            #-}+{-# LANGUAGE FlexibleInstances           #-}+{-# LANGUAGE MultiParamTypeClasses       #-}+{-# LANGUAGE OverloadedStrings           #-}+{-# LANGUAGE StrictData                  #-}+{-# LANGUAGE TypeFamilies                #-}+{-# OPTIONS_GHC -fno-warn-name-shadowing #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Alignment.Base+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Alignment.Base ( -- * BAM version 1.6 alignment mandatory and optional data types+                                                BAM_V1_6_BAM_Alignment(..)+                                              ) where++import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.Base++import Data.ByteString+import Data.Int+import Data.Sequence+import Data.Word+import Data.Data+import Generics.Deriving.Base++-- | Custom BAM (version 1.6) @"BAM_V1_6_BAM_Alignment"@ data type.+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment = BAM_V1_6_BAM_Alignment+  { bam_v1_6_bam_alignment_block_size     :: Word32                                    -- ^ Total length of the alignment+                                                                                       -- record, excluding this field.+  , bam_v1_6_bam_alignment_refID          :: Int32                                     -- ^ Reference sequence ID, -1 <= refID <= n_ref;+                                                                                       -- -1 for a read without a mapping position.+  , bam_v1_6_bam_alignment_pos            :: Int32                                     -- ^ 0-based leftmost coordinate (= POS - 1).+  , bam_v1_6_bam_alignment_l_read_name    :: Word8                                     -- ^ Length of read_name below (= length(QNAME) + 1).+  , bam_v1_6_bam_alignment_mapq           :: Word8                                     -- ^ Mapping quality (= MAPQ).+  , bam_v1_6_bam_alignment_bin            :: Word16                                    -- ^ BAI index bin, see Section 4.2.1.+  , bam_v1_6_bam_alignment_n_cigar_op     :: Word16                                    -- ^ Number of operations in CIGAR,+                                                                                       -- see section 4.2.2.+  , bam_v1_6_bam_alignment_flag           :: Word16                                    -- ^ Bitwise flags (= FLAG).+  , bam_v1_6_bam_alignment_l_seq          :: Word32                                    -- ^ Length of SEQ.+  , bam_v1_6_bam_alignment_next_refID     :: Int32                                     -- ^ Ref-ID of the next seqment+                                                                                       -- (-1 <= next_refID <= n_ref).+  , bam_v1_6_bam_alignment_next_pos       :: Int32                                     -- ^ 0-based leftmost pos of the+                                                                                       -- next segment (= PNEXT - 1).+  , bam_v1_6_bam_alignment_tlen           :: Int32                                     -- ^ Template length (= TLEN).+  , bam_v1_6_bam_alignment_read_name      :: ByteString                                -- ^ Read name; NUL-terminated+                                                                                       -- (QNAME with trailing 0x00/'\0').+  , bam_v1_6_bam_alignment_cigar          :: Seq Word32                                -- ^ CIGAR; op_len<<4<<|op.+                                                                                       -- 'MIDNSHP=X' -> '012345678'.+  , bam_v1_6_bam_alignment_seq            :: Seq Word8                                 -- ^ 4-bit encoded read:+                                                                                       -- '=ACMGRSVTWYHKDBN' -> [0,15].+                                                                                       -- See section 4.2.3.+  , bam_v1_6_bam_alignment_qual           :: ByteString                                -- ^ Phred-scaled base qualities.+                                                                                       -- See section 4.2.3.+  , bam_v1_6_bam_alignment_optionalfields :: Seq BAM_V1_6_BAM_Alignment_OptionalFields -- ^ List of auxiliary data. +                                                                                       -- See section 4.2.4+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment where+  BAM_V1_6_BAM_Alignment bam_v1_6_bam_alignment_block_size1+                         bam_v1_6_bam_alignment_refID1+                         bam_v1_6_bam_alignment_pos1+                         bam_v1_6_bam_alignment_l_read_name1+                         bam_v1_6_bam_alignment_mapq1+                         bam_v1_6_bam_alignment_bin1+                         bam_v1_6_bam_alignment_n_cigar_op1+                         bam_v1_6_bam_alignment_flag1+                         bam_v1_6_bam_alignment_l_seq1+                         bam_v1_6_bam_alignment_next_refID1+                         bam_v1_6_bam_alignment_next_pos1+                         bam_v1_6_bam_alignment_tlen1+                         bam_v1_6_bam_alignment_read_name1+                         bam_v1_6_bam_alignment_cigar1+                         bam_v1_6_bam_alignment_seq1+                         bam_v1_6_bam_alignment_qual1+                         bam_v1_6_bam_alignment_optional_fields1 ==+    BAM_V1_6_BAM_Alignment bam_v1_6_bam_alignment_block_size2+                           bam_v1_6_bam_alignment_refID2+                           bam_v1_6_bam_alignment_pos2+                           bam_v1_6_bam_alignment_l_read_name2+                           bam_v1_6_bam_alignment_mapq2+                           bam_v1_6_bam_alignment_bin2+                           bam_v1_6_bam_alignment_n_cigar_op2+                           bam_v1_6_bam_alignment_flag2+                           bam_v1_6_bam_alignment_l_seq2+                           bam_v1_6_bam_alignment_next_refID2+                           bam_v1_6_bam_alignment_next_pos2+                           bam_v1_6_bam_alignment_tlen2+                           bam_v1_6_bam_alignment_read_name2+                           bam_v1_6_bam_alignment_cigar2+                           bam_v1_6_bam_alignment_seq2+                           bam_v1_6_bam_alignment_qual2+                           bam_v1_6_bam_alignment_optional_fields2 =+      bam_v1_6_bam_alignment_block_size1      ==  bam_v1_6_bam_alignment_block_size2  &&+      bam_v1_6_bam_alignment_refID1           ==  bam_v1_6_bam_alignment_refID2       &&+      bam_v1_6_bam_alignment_pos1             ==  bam_v1_6_bam_alignment_pos2         &&+      bam_v1_6_bam_alignment_l_read_name1     ==  bam_v1_6_bam_alignment_l_read_name2 &&+      bam_v1_6_bam_alignment_mapq1            ==  bam_v1_6_bam_alignment_mapq2        &&+      bam_v1_6_bam_alignment_bin1             ==  bam_v1_6_bam_alignment_bin2         &&+      bam_v1_6_bam_alignment_n_cigar_op1      ==  bam_v1_6_bam_alignment_n_cigar_op2  &&+      bam_v1_6_bam_alignment_flag1            ==  bam_v1_6_bam_alignment_flag2        &&+      bam_v1_6_bam_alignment_l_seq1           ==  bam_v1_6_bam_alignment_l_seq2       &&+      bam_v1_6_bam_alignment_next_refID1      ==  bam_v1_6_bam_alignment_next_refID2  &&+      bam_v1_6_bam_alignment_next_pos1        ==  bam_v1_6_bam_alignment_next_pos2    &&+      bam_v1_6_bam_alignment_tlen1            ==  bam_v1_6_bam_alignment_tlen2        &&+      bam_v1_6_bam_alignment_read_name1       ==  bam_v1_6_bam_alignment_read_name2   &&+      bam_v1_6_bam_alignment_cigar1           ==  bam_v1_6_bam_alignment_cigar2       &&+      bam_v1_6_bam_alignment_seq1             ==  bam_v1_6_bam_alignment_seq2         &&+      bam_v1_6_bam_alignment_qual1            ==  bam_v1_6_bam_alignment_qual2        &&+      bam_v1_6_bam_alignment_optional_fields1 ==  bam_v1_6_bam_alignment_optional_fields2++instance Show BAM_V1_6_BAM_Alignment where+  show ( BAM_V1_6_BAM_Alignment block_size+                                refID+                                pos+                                l_read_name+                                mapq+                                bin+                                n_cigar_op+                                flag+                                l_seq+                                next_refID+                                next_pos+                                tlen+                                read_name+                                cigar+                                seq+                                qual+                                optionalfields+       ) =+    "BAM_V1_6_BAM_Alignment { "                   +++    "bam_v1_6_bam_alignment_block_size = "        +++    (show block_size)                             +++    " , bam_v1_6_bam_alignment_refID = "          +++    (show refID)                                  +++    " , bam_v1_6_bam_alignment_pos = "            +++    (show pos)                                    +++    " , bam_v1_6_bam_alignment_l_read_name = "    +++    (show l_read_name)                            +++    " , bam_v1_6_bam_alignment_mapq = "           +++    (show mapq)                                   +++    " , bam_v1_6_bam_alignment_bin = "            +++    (show bin)                                    +++    " , bam_v1_6_bam_alignment_n_cigar_op = "     +++    (show n_cigar_op)                             +++    " , bam_v1_6_bam_alignment_flag = "           +++    (show flag)                                   +++    " , bam_v1_6_bam_alignment_l_seq = "          +++    (show l_seq)                                  +++    " , bam_v1_6_bam_alignment_next_refID = "     +++    (show next_refID)                             +++    " , bam_v1_6_bam_alignment_next_pos = "       +++    (show next_pos)                               +++    " , bam_v1_6_bam_alignment_tlen = "           +++    (show tlen)                                   +++    " , bam_v1_6_bam_alignment_read_name = "      +++    (show read_name)                              +++    " , bam_v1_6_bam_alignment_cigar = "          +++    (show cigar)                                  +++    " , bam_v1_6_bam_alignment_seq = "            +++    (show seq)                                    +++    " , bam_v1_6_bam_alignment_qual = "           +++    (show qual)                                   +++    " , bam_v1_6_bam_alignment_optionalfields = " +++    (show optionalfields)                         +++    " }"

@@ -0,0 +1,72 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Alignment.OptionalFields.AOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Alignment.OptionalFields.AOPT ( -- * BAM version 1.6 alignment optional fields data type+                                                               BAM_V1_6_BAM_Alignment_OptionalFields_AOPT(..)+                                                             ) where++import Data.ByteString+import Data.Word+import Data.Data+import Generics.Deriving.Base+++-- | Custom BAM (version 1.6) @"BAM_V1_6_Alignment_OptionalFields_AOPT"@ data type.+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields_AOPT = BAM_V1_6_BAM_Alignment_OptionalFields_AOPT+  { bam_v1_6_bam_alignment_optionalfields_aopt_tag   :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_aopt_value :: Word8+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields_AOPT where+  BAM_V1_6_BAM_Alignment_OptionalFields_AOPT bam_v1_6_bam_alignment_optionalfields_aopt_tag1+                                             bam_v1_6_bam_alignment_optionalfields_aopt_value1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields_AOPT bam_v1_6_bam_alignment_optionalfields_aopt_tag2+                                               bam_v1_6_bam_alignment_optionalfields_aopt_value2 =+      bam_v1_6_bam_alignment_optionalfields_aopt_tag1   == bam_v1_6_bam_alignment_optionalfields_aopt_tag2 &&+      bam_v1_6_bam_alignment_optionalfields_aopt_value1 == bam_v1_6_bam_alignment_optionalfields_aopt_value2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields_AOPT where+  show (BAM_V1_6_BAM_Alignment_OptionalFields_AOPT tag+                                                   value+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields_AOPT { "          +++    "bam_v1_6_bam_alignment_optionalfields_aopt_tag = "      +++    (show tag)                                               +++    " , bam_v1_6_bam_alignment_optionalfields_aopt_value = " +++    (show value)                                             +++    " }"

@@ -0,0 +1,416 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BOPT ( -- * SAM version 1.6 alignment optional fields data type+                                                               BAM_V1_6_BAM_Alignment_OptionalFields_BOPT(..),+                                                               BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8(..),+                                                               BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8(..),+                                                               BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16(..),+                                                               BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16(..),+                                                               BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32(..),+                                                               BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32(..),+                                                               BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float(..),+                                                               BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_SumType(..)+                                                             ) where++import Data.ByteString hiding (count)+import Data.Data+import Data.Int+import Data.Sequence+import Data.Word+import Generics.Deriving.Base++-- | Custom BAM (version 1.6) @"BAM_V1_6_BAM_Alignment_OptionalFields_BOPT"@ data type.+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields_BOPT = BAM_V1_6_BAM_Alignment_OptionalFields_BOPT+  { bam_v1_6_bam_alignment_optionalfields_bopt_int8   :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8+  , bam_v1_6_bam_alignment_optionalfields_bopt_word8  :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8+  , bam_v1_6_bam_alignment_optionalfields_bopt_int16  :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16+  , bam_v1_6_bam_alignment_optionalfields_bopt_word16 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16+  , bam_v1_6_bam_alignment_optionalfields_bopt_int32  :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32+  , bam_v1_6_bam_alignment_optionalfields_bopt_word32 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32+  , bam_v1_6_bam_alignment_optionalfields_bopt_float  :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields_BOPT where+  BAM_V1_6_BAM_Alignment_OptionalFields_BOPT bam_v1_6_bam_alignment_optionalfields_bopt_int81+                                             bam_v1_6_bam_alignment_optionalfields_bopt_word81+                                             bam_v1_6_bam_alignment_optionalfields_bopt_int161+                                             bam_v1_6_bam_alignment_optionalfields_bopt_word161+                                             bam_v1_6_bam_alignment_optionalfields_bopt_int321+                                             bam_v1_6_bam_alignment_optionalfields_bopt_word321+                                             bam_v1_6_bam_alignment_optionalfields_bopt_float1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields_BOPT bam_v1_6_bam_alignment_optionalfields_bopt_int82+                                               bam_v1_6_bam_alignment_optionalfields_bopt_word82+                                               bam_v1_6_bam_alignment_optionalfields_bopt_int162+                                               bam_v1_6_bam_alignment_optionalfields_bopt_word162+                                               bam_v1_6_bam_alignment_optionalfields_bopt_int322+                                               bam_v1_6_bam_alignment_optionalfields_bopt_word322+                                               bam_v1_6_bam_alignment_optionalfields_bopt_float2 =+      bam_v1_6_bam_alignment_optionalfields_bopt_int81   == bam_v1_6_bam_alignment_optionalfields_bopt_int82   &&+      bam_v1_6_bam_alignment_optionalfields_bopt_word81  == bam_v1_6_bam_alignment_optionalfields_bopt_word82  &&+      bam_v1_6_bam_alignment_optionalfields_bopt_int161  == bam_v1_6_bam_alignment_optionalfields_bopt_int162  &&+      bam_v1_6_bam_alignment_optionalfields_bopt_word161 == bam_v1_6_bam_alignment_optionalfields_bopt_word162 &&+      bam_v1_6_bam_alignment_optionalfields_bopt_int321  == bam_v1_6_bam_alignment_optionalfields_bopt_int322  &&+      bam_v1_6_bam_alignment_optionalfields_bopt_word321 == bam_v1_6_bam_alignment_optionalfields_bopt_word322 &&+      bam_v1_6_bam_alignment_optionalfields_bopt_float1  == bam_v1_6_bam_alignment_optionalfields_bopt_float2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields_BOPT where+  show (BAM_V1_6_BAM_Alignment_OptionalFields_BOPT int8+                                                   word8+                                                   int16+                                                   word16+                                                   int32+                                                   word32+                                                   float+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields_BOPT { "           +++    "bam_v1_6_bam_alignment_optionalfields_bopt_int8 = "      +++    (show int8)                                               +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_word8 = "  +++    (show word8)                                              +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_int16 = "  +++    (show int16)                                              +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_word16 = " +++    (show word16)                                             +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_int32 = "  +++    (show int32)                                              +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_word32 = " +++    (show word32)                                             +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_float = "  +++    (show float)                                              +++    " }"++-- | __c__CsSiIf of the last optional field (type B).+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8 = BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8+  { bam_v1_6_bam_alignment_optionalfields_bopt_int8_tag   :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_bopt_int8_type  :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_bopt_int8_count :: Word32+  , bam_v1_6_bam_alignment_optionalfields_bopt_int8_value :: Seq Int8+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8 where+  BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8 bam_v1_6_bam_alignment_optionalfields_bopt_int8_tag1+                                                  bam_v1_6_bam_alignment_optionalfields_bopt_int8_type1+                                                  bam_v1_6_bam_alignment_optionalfields_bopt_int8_count1+                                                  bam_v1_6_bam_alignment_optionalfields_bopt_int8_value1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8 bam_v1_6_bam_alignment_optionalfields_bopt_int8_tag2+                                                    bam_v1_6_bam_alignment_optionalfields_bopt_int8_type2+                                                    bam_v1_6_bam_alignment_optionalfields_bopt_int8_count2+                                                    bam_v1_6_bam_alignment_optionalfields_bopt_int8_value2 =+      bam_v1_6_bam_alignment_optionalfields_bopt_int8_tag1 == bam_v1_6_bam_alignment_optionalfields_bopt_int8_tag2     &&+      bam_v1_6_bam_alignment_optionalfields_bopt_int8_type1 == bam_v1_6_bam_alignment_optionalfields_bopt_int8_type2   &&+      bam_v1_6_bam_alignment_optionalfields_bopt_int8_count1 == bam_v1_6_bam_alignment_optionalfields_bopt_int8_count2 &&+      bam_v1_6_bam_alignment_optionalfields_bopt_int8_value1 == bam_v1_6_bam_alignment_optionalfields_bopt_int8_value2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8 where+  show (BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8 tag+                                                        bopttype+                                                        count+                                                        value+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8 { "          +++    "bam_v1_6_bam_alignment_optionalfields_bopt_int8_tag  = "     +++    (show tag)                                                    +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_int8_type = "  +++    (show bopttype)                                               +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_int8_count = " +++    (show count)                                                  +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_int8_value = " +++    (show value)                                                  +++    " }"++-- | c__C__sSiIf of the last optional field (type B).+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8 = BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8+  { bam_v1_6_bam_alignment_optionalfields_bopt_word8_tag   :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_bopt_word8_type  :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_bopt_word8_count :: Word32+  , bam_v1_6_bam_alignment_optionalfields_bopt_word8_value :: Seq Word8+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8 where+  BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8 bam_v1_6_bam_alignment_optionalfields_bopt_word8_tag1+                                                   bam_v1_6_bam_alignment_optionalfields_bopt_word8_type1+                                                   bam_v1_6_bam_alignment_optionalfields_bopt_word8_count1+                                                   bam_v1_6_bam_alignment_optionalfields_bopt_word8_value1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8 bam_v1_6_bam_alignment_optionalfields_bopt_word8_tag2+                                                     bam_v1_6_bam_alignment_optionalfields_bopt_word8_type2+                                                     bam_v1_6_bam_alignment_optionalfields_bopt_word8_count2+                                                     bam_v1_6_bam_alignment_optionalfields_bopt_word8_value2 =+      bam_v1_6_bam_alignment_optionalfields_bopt_word8_tag1 == bam_v1_6_bam_alignment_optionalfields_bopt_word8_tag2     &&+      bam_v1_6_bam_alignment_optionalfields_bopt_word8_type1 == bam_v1_6_bam_alignment_optionalfields_bopt_word8_type2   &&+      bam_v1_6_bam_alignment_optionalfields_bopt_word8_count1 == bam_v1_6_bam_alignment_optionalfields_bopt_word8_count2 &&+      bam_v1_6_bam_alignment_optionalfields_bopt_word8_value1 == bam_v1_6_bam_alignment_optionalfields_bopt_word8_value2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8 where+  show (BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8 tag+                                                         bopttype+                                                         count+                                                         value+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8 { "          +++    "bam_v1_6_bam_alignment_optionalfields_bopt_word8_tag  = "     +++    (show tag)                                                     +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_word8_type = "  +++    (show bopttype)                                                +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_word8_count = " +++    (show count)                                                   +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_word8_value = " +++    (show value)                                                   +++    " }"++-- | cC__s__SiIf of the last optional field (type B).+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16 = BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16+  { bam_v1_6_bam_alignment_optionalfields_bopt_int16_tag   :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_bopt_int16_type  :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_bopt_int16_count :: Word32+  , bam_v1_6_bam_alignment_optionalfields_bopt_int16_value :: Seq Int16+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16 where+  BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16 bam_v1_6_bam_alignment_optionalfields_bopt_int16_tag1+                                                   bam_v1_6_bam_alignment_optionalfields_bopt_int16_type1+                                                   bam_v1_6_bam_alignment_optionalfields_bopt_int16_count1+                                                   bam_v1_6_bam_alignment_optionalfields_bopt_int16_value1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16 bam_v1_6_bam_alignment_optionalfields_bopt_int16_tag2+                                                     bam_v1_6_bam_alignment_optionalfields_bopt_int16_type2+                                                     bam_v1_6_bam_alignment_optionalfields_bopt_int16_count2+                                                     bam_v1_6_bam_alignment_optionalfields_bopt_int16_value2 =+      bam_v1_6_bam_alignment_optionalfields_bopt_int16_tag1 == bam_v1_6_bam_alignment_optionalfields_bopt_int16_tag2     &&+      bam_v1_6_bam_alignment_optionalfields_bopt_int16_type1 == bam_v1_6_bam_alignment_optionalfields_bopt_int16_type2   &&+      bam_v1_6_bam_alignment_optionalfields_bopt_int16_count1 == bam_v1_6_bam_alignment_optionalfields_bopt_int16_count2 &&+      bam_v1_6_bam_alignment_optionalfields_bopt_int16_value1 == bam_v1_6_bam_alignment_optionalfields_bopt_int16_value2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16 where+  show (BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16 tag+                                                         bopttype+                                                         count+                                                         value+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16 { "          +++    "bam_v1_6_bam_alignment_optionalfields_bopt_int16_tag  = "     +++    (show tag)                                                     +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_int16_type = "  +++    (show bopttype)                                                +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_int16_count = " +++    (show count)                                                   +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_int16_value = " +++    (show value)                                                   +++    " }"++-- | cCs__S__iIf of the last optional field (type B).+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16 = BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16+  { bam_v1_6_bam_alignment_optionalfields_bopt_word16_tag   :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_bopt_word16_type  :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_bopt_word16_count :: Word32+  , bam_v1_6_bam_alignment_optionalfields_bopt_word16_value :: Seq Word16+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16 where+  BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16 bam_v1_6_bam_alignment_optionalfields_bopt_word16_tag1+                                                    bam_v1_6_bam_alignment_optionalfields_bopt_word16_type1+                                                    bam_v1_6_bam_alignment_optionalfields_bopt_word16_count1+                                                    bam_v1_6_bam_alignment_optionalfields_bopt_word16_value1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16 bam_v1_6_bam_alignment_optionalfields_bopt_word16_tag2+                                                      bam_v1_6_bam_alignment_optionalfields_bopt_word16_type2+                                                      bam_v1_6_bam_alignment_optionalfields_bopt_word16_count2+                                                      bam_v1_6_bam_alignment_optionalfields_bopt_word16_value2 =+      bam_v1_6_bam_alignment_optionalfields_bopt_word16_tag1 == bam_v1_6_bam_alignment_optionalfields_bopt_word16_tag2     &&+      bam_v1_6_bam_alignment_optionalfields_bopt_word16_type1 == bam_v1_6_bam_alignment_optionalfields_bopt_word16_type2   &&+      bam_v1_6_bam_alignment_optionalfields_bopt_word16_count1 == bam_v1_6_bam_alignment_optionalfields_bopt_word16_count2 &&+      bam_v1_6_bam_alignment_optionalfields_bopt_word16_value1 == bam_v1_6_bam_alignment_optionalfields_bopt_word16_value2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16 where+  show (BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16 tag+                                                          bopttype+                                                          count+                                                          value+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16 { "          +++    "bam_v1_6_bam_alignment_optionalfields_bopt_word16_tag  = "     +++    (show tag)                                                      +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_word16_type = "  +++    (show bopttype)                                                 +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_word16_count = " +++    (show count)                                                    +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_word16_value = " +++    (show value)                                                    +++    " }"++-- | cCsS__i__If of the last optional field (type B).+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32 = BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32+  { bam_v1_6_bam_alignment_optionalfields_bopt_int32_tag   :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_bopt_int32_type  :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_bopt_int32_count :: Word32+  , bam_v1_6_bam_alignment_optionalfields_bopt_int32_value :: Seq Int32+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32 where+  BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32 bam_v1_6_bam_alignment_optionalfields_bopt_int32_tag1+                                                   bam_v1_6_bam_alignment_optionalfields_bopt_int32_type1+                                                   bam_v1_6_bam_alignment_optionalfields_bopt_int32_count1+                                                   bam_v1_6_bam_alignment_optionalfields_bopt_int32_value1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32 bam_v1_6_bam_alignment_optionalfields_bopt_int32_tag2+                                                     bam_v1_6_bam_alignment_optionalfields_bopt_int32_type2+                                                     bam_v1_6_bam_alignment_optionalfields_bopt_int32_count2+                                                     bam_v1_6_bam_alignment_optionalfields_bopt_int32_value2 =+      bam_v1_6_bam_alignment_optionalfields_bopt_int32_tag1 == bam_v1_6_bam_alignment_optionalfields_bopt_int32_tag2     &&+      bam_v1_6_bam_alignment_optionalfields_bopt_int32_type1 == bam_v1_6_bam_alignment_optionalfields_bopt_int32_type2   &&+      bam_v1_6_bam_alignment_optionalfields_bopt_int32_count1 == bam_v1_6_bam_alignment_optionalfields_bopt_int32_count2 &&+      bam_v1_6_bam_alignment_optionalfields_bopt_int32_value1 == bam_v1_6_bam_alignment_optionalfields_bopt_int32_value2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32 where+  show (BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32 tag+                                                         bopttype+                                                         count+                                                         value+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32 { "          +++    "bam_v1_6_bam_alignment_optionalfields_bopt_int32_tag  = "     +++    (show tag)                                                     +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_int32_type = "  +++    (show bopttype)                                                +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_int32_count = " +++    (show count)                                                   +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_int32_value = " +++    (show value)                                                   +++    " }"++-- | cCsSi__I__f of the last optional field (type B).+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32 = BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32+  { bam_v1_6_bam_alignment_optionalfields_bopt_word32_tag   :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_bopt_word32_type  :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_bopt_word32_count :: Word32+  , bam_v1_6_bam_alignment_optionalfields_bopt_word32_value :: Seq Word32+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32 where+  BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32 bam_v1_6_bam_alignment_optionalfields_bopt_word32_tag1+                                                    bam_v1_6_bam_alignment_optionalfields_bopt_word32_type1+                                                    bam_v1_6_bam_alignment_optionalfields_bopt_word32_count1+                                                    bam_v1_6_bam_alignment_optionalfields_bopt_word32_value1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32 bam_v1_6_bam_alignment_optionalfields_bopt_word32_tag2+                                                      bam_v1_6_bam_alignment_optionalfields_bopt_word32_type2+                                                      bam_v1_6_bam_alignment_optionalfields_bopt_word32_count2+                                                      bam_v1_6_bam_alignment_optionalfields_bopt_word32_value2 =+      bam_v1_6_bam_alignment_optionalfields_bopt_word32_tag1 == bam_v1_6_bam_alignment_optionalfields_bopt_word32_tag2     &&+      bam_v1_6_bam_alignment_optionalfields_bopt_word32_type1 == bam_v1_6_bam_alignment_optionalfields_bopt_word32_type2   &&+      bam_v1_6_bam_alignment_optionalfields_bopt_word32_count1 == bam_v1_6_bam_alignment_optionalfields_bopt_word32_count2 &&+      bam_v1_6_bam_alignment_optionalfields_bopt_word32_value1 == bam_v1_6_bam_alignment_optionalfields_bopt_word32_value2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32 where+  show (BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32 tag+                                                          bopttype+                                                          count+                                                          value+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32 { "          +++    "bam_v1_6_bam_alignment_optionalfields_bopt_word32_tag  = "     +++    (show tag)                                                      +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_word32_type = "  +++    (show bopttype)                                                 +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_word32_count = " +++    (show count)                                                    +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_word32_value = " +++    (show value)                                                    +++    " }"++-- | cCsSiI__f__ of the last optional field (type B).+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float = BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float+  { bam_v1_6_bam_alignment_optionalfields_bopt_float_tag   :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_bopt_float_type  :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_bopt_float_count :: Word32+  , bam_v1_6_bam_alignment_optionalfields_bopt_float_value :: Seq Float+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float where+  BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float bam_v1_6_bam_alignment_optionalfields_bopt_float_tag1+                                                   bam_v1_6_bam_alignment_optionalfields_bopt_float_type1+                                                   bam_v1_6_bam_alignment_optionalfields_bopt_float_count1+                                                   bam_v1_6_bam_alignment_optionalfields_bopt_float_value1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float bam_v1_6_bam_alignment_optionalfields_bopt_float_tag2+                                                     bam_v1_6_bam_alignment_optionalfields_bopt_float_type2+                                                     bam_v1_6_bam_alignment_optionalfields_bopt_float_count2+                                                     bam_v1_6_bam_alignment_optionalfields_bopt_float_value2 =+      bam_v1_6_bam_alignment_optionalfields_bopt_float_tag1   == bam_v1_6_bam_alignment_optionalfields_bopt_float_tag2   &&+      bam_v1_6_bam_alignment_optionalfields_bopt_float_type1  == bam_v1_6_bam_alignment_optionalfields_bopt_float_type2  &&+      bam_v1_6_bam_alignment_optionalfields_bopt_float_count1 == bam_v1_6_bam_alignment_optionalfields_bopt_float_count2 &&+      bam_v1_6_bam_alignment_optionalfields_bopt_float_value1 == bam_v1_6_bam_alignment_optionalfields_bopt_float_value2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float where+  show (BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float tag+                                                         bopttype+                                                         count+                                                         value+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float { "          +++    "bam_v1_6_bam_alignment_optionalfields_bopt_float_tag  = "     +++    (show tag)                                                     +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_float_type = "  +++    (show bopttype)                                                +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_float_count = " +++    (show count)                                                   +++    " , bam_v1_6_bam_alignment_optionalfields_bopt_float_value = " +++    (show value)                                                   +++    " }"++-- | Sum type that can represent any of the+-- BAM_V1_6_BAM_Alignment_OptionalFields_BOPT types.+data BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_SumType =+    BOPTInt8+  | BOPTWord8+  | BOPTInt16+  | BOPTWord16+  | BOPTInt32+  | BOPTWord32+  | BOPTFloat+  | BOPTEmpty+  deriving (Eq,Generic,Typeable)

@@ -0,0 +1,158 @@+{-# LANGUAGE DeriveDataTypeable          #-}+{-# LANGUAGE DeriveGeneric               #-}+{-# LANGUAGE FlexibleContexts            #-}+{-# LANGUAGE FlexibleInstances           #-}+{-# LANGUAGE MultiParamTypeClasses       #-}+{-# LANGUAGE OverloadedStrings           #-}+{-# LANGUAGE StrictData                  #-}+{-# LANGUAGE TypeFamilies                #-}+{-# OPTIONS_GHC -fno-warn-name-shadowing #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Alignment.OptionalFields.Base+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Alignment.OptionalFields.Base ( -- * BAM version 1.6 alignment optional fields data type+                                                               BAM_V1_6_BAM_Alignment_OptionalFields(..)+                                                             , BAM_V1_6_BAM_Alignment_OptionalFields_SumType(..)+                                                             ) where++import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.AOPT+import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BigCOPT+import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BigIOPT+import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BigSOPT+import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.SmallCOPT+import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.SmallIOPT+import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.SmallSOPT+import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.FOPT+import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.ZOPT+import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.HOPT+import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BOPT++import Data.Data+import Generics.Deriving.Base++-- | Custom BAM (version 1.6) @"BAM_V1_6_BAM_Alignment_Optional_Fields"@ data type.+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields = BAM_V1_6_BAM_Alignment_OptionalFields+  { bam_v1_6_bam_alignment_optionalfields_aopt        :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_AOPT      -- ^ A - [!-~] -+                                                                                                               -- Printable character.+  , bam_v1_6_bam_alignment_optionalfields_smallcopt   :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_SmallCOPT -- c - [0-9]+ -+                                                                                                               -- Int8 (signed).+  , bam_v1_6_bam_alignment_optionalfields_bigcopt     :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BigCOPT   -- C - [0-9]+ -+                                                                                                               -- Word8 (unsigned).+  , bam_v1_6_bam_alignment_optionalfields_smalliopt   :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT -- i - [0-9]+ -+                                                                                                               -- Int32 (signed).+  , bam_v1_6_bam_alignment_optionalfields_bigiopt     :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT   -- I - [0-9]+ -+                                                                                                               -- Word32 (unsigned).+  , bam_v1_6_bam_alignment_optionalfields_smallsopt   :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_SmallSOPT -- s - [0-9]+ -+                                                                                                               -- Int16 (signed).+  , bam_v1_6_bam_alignment_optionalfields_bigsopt     :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BigSOPT   -- S - [0-9]+ -+                                                                                                               -- Word16 (unsigned).+  , bam_v1_6_bam_alignment_optionalfields_fopt        :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_FOPT      -- ^ f - [-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? -+                                                                                                               -- Single-precision floating number.+  , bam_v1_6_bam_alignment_optionalfields_zopt        :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_ZOPT      -- ^ Z - [ !-~]* -+                                                                                                               -- Printable string, including space.+  , bam_v1_6_bam_alignment_optionalfields_hopt        :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_HOPT      -- ^ H - ([0-9A-F][0-9A-F])* -+                                                                                                               -- Byte array in the Hex format.+  , bam_v1_6_bam_alignment_optionalfields_bopt        :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT      -- ^ B - [cCsSiIf]​(,[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* -+                                                                                                               -- Integer or numeric array.+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields where+  BAM_V1_6_BAM_Alignment_OptionalFields bam_v1_6_bam_alignment_optionalfields_aopt1+                                        bam_v1_6_bam_alignment_optionalfields_smallcopt1+                                        bam_v1_6_bam_alignment_optionalfields_bigcopt1+                                        bam_v1_6_bam_alignment_optionalfields_smalliopt1+                                        bam_v1_6_bam_alignment_optionalfields_bigiopt1+                                        bam_v1_6_bam_alignment_optionalfields_smallsopt1+                                        bam_v1_6_bam_alignment_optionalfields_bigsopt1+                                        bam_v1_6_bam_alignment_optionalfields_fopt1+                                        bam_v1_6_bam_alignment_optionalfields_zopt1+                                        bam_v1_6_bam_alignment_optionalfields_hopt1+                                        bam_v1_6_bam_alignment_optionalfields_bopt1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields bam_v1_6_bam_alignment_optionalfields_aopt2+                                          bam_v1_6_bam_alignment_optionalfields_smallcopt2+                                          bam_v1_6_bam_alignment_optionalfields_bigcopt2+                                          bam_v1_6_bam_alignment_optionalfields_smalliopt2+                                          bam_v1_6_bam_alignment_optionalfields_bigiopt2+                                          bam_v1_6_bam_alignment_optionalfields_smallsopt2+                                          bam_v1_6_bam_alignment_optionalfields_bigsopt2+                                          bam_v1_6_bam_alignment_optionalfields_fopt2+                                          bam_v1_6_bam_alignment_optionalfields_zopt2+                                          bam_v1_6_bam_alignment_optionalfields_hopt2+                                          bam_v1_6_bam_alignment_optionalfields_bopt2 =+      bam_v1_6_bam_alignment_optionalfields_aopt1      ==  bam_v1_6_bam_alignment_optionalfields_aopt2        &&+      bam_v1_6_bam_alignment_optionalfields_smallcopt1 ==  bam_v1_6_bam_alignment_optionalfields_smallcopt2   &&+      bam_v1_6_bam_alignment_optionalfields_bigcopt1   ==  bam_v1_6_bam_alignment_optionalfields_bigcopt2     &&+      bam_v1_6_bam_alignment_optionalfields_smalliopt1 ==  bam_v1_6_bam_alignment_optionalfields_smalliopt2   &&+      bam_v1_6_bam_alignment_optionalfields_bigiopt1   ==  bam_v1_6_bam_alignment_optionalfields_bigiopt2     &&+      bam_v1_6_bam_alignment_optionalfields_smallsopt1 ==  bam_v1_6_bam_alignment_optionalfields_smallsopt2   &&+      bam_v1_6_bam_alignment_optionalfields_bigsopt1   ==  bam_v1_6_bam_alignment_optionalfields_bigsopt2     &&+      bam_v1_6_bam_alignment_optionalfields_fopt1      ==  bam_v1_6_bam_alignment_optionalfields_fopt2        &&+      bam_v1_6_bam_alignment_optionalfields_zopt1      ==  bam_v1_6_bam_alignment_optionalfields_zopt2        &&+      bam_v1_6_bam_alignment_optionalfields_hopt1      ==  bam_v1_6_bam_alignment_optionalfields_hopt2        &&+      bam_v1_6_bam_alignment_optionalfields_bopt1      ==  bam_v1_6_bam_alignment_optionalfields_bopt2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields where+  show ( BAM_V1_6_BAM_Alignment_OptionalFields aopt+                                                smallcopt+                                                bigcopt+                                                smalliopt+                                                bigiopt+                                                smallsopt+                                                bigsopt+                                                fopt+                                                zopt+                                                hopt+                                                bopt+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields { "             +++    "bam_v1_6_bam_alignment_optionalfields_aopt = "         +++    (show aopt)                                             +++    " , bam_v1_6_bam_alignment_optionalfields_smallcopt = " +++    (show smallcopt)                                        +++    " , bam_v1_6_bam_alignment_optionalfields_bigcopt = "   +++    (show bigcopt)                                          +++    " , bam_v1_6_bam_alignment_optionalfields_smalliopt = " +++    (show smalliopt)                                        +++    " , bam_v1_6_bam_alignment_optionalfields_bigiopt = "   +++    (show bigiopt)                                          +++    " , bam_v1_6_bam_alignment_optionalfields_smallsopt = " +++    (show smallsopt)                                        +++    " , bam_v1_6_bam_alignment_optionalfields_bigsopt = "   +++    (show bigsopt)                                          +++    " , bam_v1_6_bam_alignment_optionalfields_fopt = "      +++    (show fopt)                                             +++    " , bam_v1_6_bam_alignment_optionalfields_zopt = "      +++    (show zopt)                                             +++    " , bam_v1_6_bam_alignment_optionalfields_hopt = "      +++    (show hopt)                                             +++    " , bam_v1_6_bam_alignment_optionalfields_bopt = "      +++    (show bopt)                                             +++    " }"++-- | Sum type that can represent any of the+-- BAM_V1_6_BAM_Alignment_OptionalFields types.+data BAM_V1_6_BAM_Alignment_OptionalFields_SumType =+    AOPT+  | SmallCOPT+  | BigCOPT+  | SmallIOPT+  | BigIOPT+  | SmallSOPT+  | BigSOPT+  | FOPT+  | ZOPT+  | HOPT+  | BOPT+  | Empty+  deriving (Eq,Generic,Typeable)

@@ -0,0 +1,71 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BigCOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BigCOPT ( -- * BAM version 1.6 alignment optional fields data type+                                                                  BAM_V1_6_BAM_Alignment_OptionalFields_BigCOPT(..)+                                                                ) where++import Data.ByteString+import Data.Word+import Data.Data+import Generics.Deriving.Base++-- | Custom BAM (version 1.6) @"BAM_V1_6_Alignment_OptionalFields_BigCOPT"@ data type.+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields_BigCOPT = BAM_V1_6_BAM_Alignment_OptionalFields_BigCOPT+  { bam_v1_6_bam_alignment_optionalfields_bigcopt_tag   :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_bigcopt_value :: Word8+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields_BigCOPT where+  BAM_V1_6_BAM_Alignment_OptionalFields_BigCOPT bam_v1_6_bam_alignment_optionalfields_bigcopt_tag1+                                                bam_v1_6_bam_alignment_optionalfields_bigcopt_value1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields_BigCOPT bam_v1_6_bam_alignment_optionalfields_bigcopt_tag2+                                                  bam_v1_6_bam_alignment_optionalfields_bigcopt_value2 =+      bam_v1_6_bam_alignment_optionalfields_bigcopt_tag1   == bam_v1_6_bam_alignment_optionalfields_bigcopt_tag2 &&+      bam_v1_6_bam_alignment_optionalfields_bigcopt_value1 == bam_v1_6_bam_alignment_optionalfields_bigcopt_value2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields_BigCOPT where+  show (BAM_V1_6_BAM_Alignment_OptionalFields_BigCOPT tag+                                                      value+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields_BigCOPT { "          +++    "bam_v1_6_bam_alignment_optionalfields_bigcopt_tag = "      +++    (show tag)                                                  +++    " , bam_v1_6_bam_alignment_optionalfields_bigcopt_value = " +++    (show value)                                                +++    " }"

@@ -0,0 +1,71 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BigIOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BigIOPT ( -- * BAM version 1.6 alignment optional fields data type+                                                                  BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT(..)+                                                                ) where++import Data.ByteString+import Data.Word+import Data.Data+import Generics.Deriving.Base++-- | Custom BAM (version 1.6) @"BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT"@ data type.+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT = BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT+  { bam_v1_6_bam_alignment_optionalfields_bigiopt_tag   :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_bigiopt_value :: Word32+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT where+  BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT bam_v1_6_bam_alignment_optionalfields_bigiopt_tag1+                                                bam_v1_6_bam_alignment_optionalfields_bigiopt_value1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT bam_v1_6_bam_alignment_optionalfields_bigiopt_tag2+                                                  bam_v1_6_bam_alignment_optionalfields_bigiopt_value2 =+      bam_v1_6_bam_alignment_optionalfields_bigiopt_tag1   == bam_v1_6_bam_alignment_optionalfields_bigiopt_tag2 &&+      bam_v1_6_bam_alignment_optionalfields_bigiopt_value1 == bam_v1_6_bam_alignment_optionalfields_bigiopt_value2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT where+  show (BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT tag+                                                      value+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT { "          +++    "bam_v1_6_bam_alignment_optionalfields_bigiopt_tag = "      +++    (show tag)                                                  +++    " , bam_v1_6_bam_alignment_optionalfields_bigiopt_value = " +++    (show value)                                                +++    " }"

@@ -0,0 +1,71 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BigSOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BigSOPT ( -- * BAM version 1.6 alignment optional fields data type+                                                                  BAM_V1_6_BAM_Alignment_OptionalFields_BigSOPT(..)+                                                                ) where++import Data.ByteString+import Data.Word+import Data.Data+import Generics.Deriving.Base++-- | Custom BAM (version 1.6) @"BAM_V1_6_Alignment_OptionalFields_BigSOPT"@ data type.+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields_BigSOPT = BAM_V1_6_BAM_Alignment_OptionalFields_BigSOPT+  { bam_v1_6_bam_alignment_optionalfields_bigsopt_tag   :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_bigsopt_value :: Word16+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields_BigSOPT where+  BAM_V1_6_BAM_Alignment_OptionalFields_BigSOPT bam_v1_6_bam_alignment_optionalfields_bigsopt_tag1+                                                bam_v1_6_bam_alignment_optionalfields_bigsopt_value1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields_BigSOPT bam_v1_6_bam_alignment_optionalfields_bigsopt_tag2+                                                  bam_v1_6_bam_alignment_optionalfields_bigsopt_value2 =+      bam_v1_6_bam_alignment_optionalfields_bigsopt_tag1   == bam_v1_6_bam_alignment_optionalfields_bigsopt_tag2 &&+      bam_v1_6_bam_alignment_optionalfields_bigsopt_value1 == bam_v1_6_bam_alignment_optionalfields_bigsopt_value2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields_BigSOPT where+  show (BAM_V1_6_BAM_Alignment_OptionalFields_BigSOPT tag+                                                      value+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields_BigSOPT { "          +++    "bam_v1_6_bam_alignment_optionalfields_bigsopt_tag = "      +++    (show tag)                                                  +++    " , bam_v1_6_bam_alignment_optionalfields_bigsopt_value = " +++    (show value)                                                +++    " }"

@@ -0,0 +1,71 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Alignment.OptionalFields.FOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Alignment.OptionalFields.FOPT ( -- * BAM version 1.6 alignment optional fields data type+                                                               BAM_V1_6_BAM_Alignment_OptionalFields_FOPT(..)+                                                             ) where++import Data.ByteString+import Data.Word+import Data.Data+import Generics.Deriving.Base++-- | Custom BAM (version 1.6) @"BAM_V1_6_Alignment_OptionalFields_FOPT"@ data type.+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields_FOPT = BAM_V1_6_BAM_Alignment_OptionalFields_FOPT+  { bam_v1_6_bam_alignment_optionalfields_fopt_tag   :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_fopt_value :: Word32+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields_FOPT where+  BAM_V1_6_BAM_Alignment_OptionalFields_FOPT bam_v1_6_bam_alignment_optionalfields_fopt_tag1+                                             bam_v1_6_bam_alignment_optionalfields_fopt_value1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields_FOPT bam_v1_6_bam_alignment_optionalfields_fopt_tag2+                                               bam_v1_6_bam_alignment_optionalfields_fopt_value2 =+      bam_v1_6_bam_alignment_optionalfields_fopt_tag1 == bam_v1_6_bam_alignment_optionalfields_fopt_tag2 &&+      bam_v1_6_bam_alignment_optionalfields_fopt_value1 == bam_v1_6_bam_alignment_optionalfields_fopt_value2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields_FOPT where+  show (BAM_V1_6_BAM_Alignment_OptionalFields_FOPT tag+                                                   value+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields_FOPT { "          +++    "bam_v1_6_bam_alignment_optionalfields_fopt_tag = "      +++    (show tag)                                               +++    " , bam_v1_6_bam_alignment_optionalfields_fopt_value = " +++    (show value)                                             +++    " }"

@@ -0,0 +1,71 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Alignment.OptionalFields.HOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Alignment.OptionalFields.HOPT ( -- * BAM version 1.6 alignment optional fields data type+                                                               BAM_V1_6_BAM_Alignment_OptionalFields_HOPT(..)+                                                             ) where++import Data.ByteString (ByteString)+import Data.Data+import Data.Sequence+import Generics.Deriving.Base++-- | Custom BAM (version 1.6) @"BAM_V1_6_Alignment_OptionalFields_HOPT"@ data type.+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields_HOPT = BAM_V1_6_BAM_Alignment_OptionalFields_HOPT+  { bam_v1_6_bam_alignment_optionalfields_hopt_tag   :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_hopt_value :: Seq ByteString+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields_HOPT where+  BAM_V1_6_BAM_Alignment_OptionalFields_HOPT bam_v1_6_bam_alignment_optionalfields_hopt_tag1+                                             bam_v1_6_bam_alignment_optionalfields_hopt_value1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields_HOPT bam_v1_6_bam_alignment_optionalfields_hopt_tag2+                                               bam_v1_6_bam_alignment_optionalfields_hopt_value2 =+      bam_v1_6_bam_alignment_optionalfields_hopt_tag1   == bam_v1_6_bam_alignment_optionalfields_hopt_tag2 &&+      bam_v1_6_bam_alignment_optionalfields_hopt_value1 == bam_v1_6_bam_alignment_optionalfields_hopt_value2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields_HOPT where+  show (BAM_V1_6_BAM_Alignment_OptionalFields_HOPT tag+                                                   value+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields_HOPT { "          +++    "bam_v1_6_bam_alignment_optionalfields_hopt_tag = "      +++    (show tag)                                               +++    " , bam_v1_6_bam_alignment_optionalfields_hopt_value = " +++    (show value)                                             +++    " }"

@@ -0,0 +1,71 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Alignment.OptionalFields.SmallCOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Alignment.OptionalFields.SmallCOPT ( -- * BAM version 1.6 alignment optional fields data type+                                                                    BAM_V1_6_BAM_Alignment_OptionalFields_SmallCOPT(..)+                                                                  ) where++import Data.ByteString+import Data.Int+import Data.Data+import Generics.Deriving.Base++-- | Custom BAM (version 1.6) @"BAM_V1_6_Alignment_OptionalFields_SmallCOPT"@ data type.+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields_SmallCOPT = BAM_V1_6_BAM_Alignment_OptionalFields_SmallCOPT+  { bam_v1_6_bam_alignment_optionalfields_smallcopt_tag   :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_smallcopt_value :: Int8+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields_SmallCOPT where+  BAM_V1_6_BAM_Alignment_OptionalFields_SmallCOPT bam_v1_6_bam_alignment_optionalfields_smallcopt_tag1+                                                  bam_v1_6_bam_alignment_optionalfields_smallcopt_value1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields_SmallCOPT bam_v1_6_bam_alignment_optionalfields_smallcopt_tag2+                                                    bam_v1_6_bam_alignment_optionalfields_smallcopt_value2 =+      bam_v1_6_bam_alignment_optionalfields_smallcopt_tag1   == bam_v1_6_bam_alignment_optionalfields_smallcopt_tag2 &&+      bam_v1_6_bam_alignment_optionalfields_smallcopt_value1 == bam_v1_6_bam_alignment_optionalfields_smallcopt_value2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields_SmallCOPT where+  show (BAM_V1_6_BAM_Alignment_OptionalFields_SmallCOPT tag+                                                        value+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields_SmallCOPT { "          +++    "bam_v1_6_bam_alignment_optionalfields_smallcopt_tag = "      +++    (show tag)                                                    +++    " , bam_v1_6_bam_alignment_optionalfields_smallcopt_value = " +++    (show value)                                                  +++    " }"

@@ -0,0 +1,71 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Alignment.OptionalFields.SmallIOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Alignment.OptionalFields.SmallIOPT ( -- * BAM version 1.6 alignment optional fields data type+                                                                    BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT(..)+                                                                  ) where++import Data.ByteString+import Data.Int+import Data.Data+import Generics.Deriving.Base++-- | Custom BAM (version 1.6) @"BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT"@ data type.+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT = BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT+  { bam_v1_6_bam_alignment_optionalfields_smalliopt_tag   :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_smalliopt_value :: Int32+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT where+  BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT bam_v1_6_bam_alignment_optionalfields_smalliopt_tag1+                                                  bam_v1_6_bam_alignment_optionalfields_smalliopt_value1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT bam_v1_6_bam_alignment_optionalfields_smalliopt_tag2+                                                    bam_v1_6_bam_alignment_optionalfields_smalliopt_value2 =+      bam_v1_6_bam_alignment_optionalfields_smalliopt_tag1   == bam_v1_6_bam_alignment_optionalfields_smalliopt_tag2 &&+      bam_v1_6_bam_alignment_optionalfields_smalliopt_value1 == bam_v1_6_bam_alignment_optionalfields_smalliopt_value2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT where+  show (BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT tag+                                                        value+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT { "          +++    "bam_v1_6_bam_alignment_optionalfields_smalliopt_tag = "      +++    (show tag)                                                    +++    " , bam_v1_6_bam_alignment_optionalfields_smalliopt_value = " +++    (show value)                                                  +++    " }"

@@ -0,0 +1,71 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Alignment.OptionalFields.SmallSOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Alignment.OptionalFields.SmallSOPT ( -- * BAM version 1.6 alignment optional fields data type+                                                                    BAM_V1_6_BAM_Alignment_OptionalFields_SmallSOPT(..)+                                                                  ) where++import Data.ByteString+import Data.Int+import Data.Data+import Generics.Deriving.Base++-- | Custom BAM (version 1.6) @"BAM_V1_6_Alignment_OptionalFields_SmallSOPT"@ data type.+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields_SmallSOPT = BAM_V1_6_BAM_Alignment_OptionalFields_SmallSOPT+  { bam_v1_6_bam_alignment_optionalfields_smallsopt_tag   :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_smallsopt_value :: Int16+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields_SmallSOPT where+  BAM_V1_6_BAM_Alignment_OptionalFields_SmallSOPT bam_v1_6_bam_alignment_optionalfields_smallsopt_tag1+                                                  bam_v1_6_bam_alignment_optionalfields_smallsopt_value1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields_SmallSOPT bam_v1_6_bam_alignment_optionalfields_smallsopt_tag2+                                                    bam_v1_6_bam_alignment_optionalfields_smallsopt_value2 =+      bam_v1_6_bam_alignment_optionalfields_smallsopt_tag1   == bam_v1_6_bam_alignment_optionalfields_smallsopt_tag2 &&+      bam_v1_6_bam_alignment_optionalfields_smallsopt_value1 == bam_v1_6_bam_alignment_optionalfields_smallsopt_value2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields_SmallSOPT where+  show (BAM_V1_6_BAM_Alignment_OptionalFields_SmallSOPT tag+                                                        value+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields_SmallSOPT { "          +++    "bam_v1_6_bam_alignment_optionalfields_smallsopt_tag = "      +++    (show tag)                                                    +++    " , bam_v1_6_bam_alignment_optionalfields_smallsopt_value = " +++    (show value)                                                  +++    " }"

@@ -0,0 +1,72 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Alignment.OptionalFields.ZOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Alignment.OptionalFields.ZOPT ( -- * BAM version 1.6 alignment optional fields data type+                                                               BAM_V1_6_BAM_Alignment_OptionalFields_ZOPT(..)+                                                             ) where++import Data.ByteString+import Data.Word+import Data.Data+import Data.Sequence+import Generics.Deriving.Base++-- | Custom BAM (version 1.6) @"SAM_V1_6_Alignment_OptionalFields_ZOPT"@ data type.+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Alignment_OptionalFields_ZOPT = BAM_V1_6_BAM_Alignment_OptionalFields_ZOPT+  { bam_v1_6_bam_alignment_optionalfields_zopt_tag   :: ByteString+  , bam_v1_6_bam_alignment_optionalfields_zopt_value :: Seq Word8+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Alignment_OptionalFields_ZOPT where+  BAM_V1_6_BAM_Alignment_OptionalFields_ZOPT bam_v1_6_bam_alignment_optionalfields_zopt_tag1+                                             bam_v1_6_bam_alignment_optionalfields_zopt_value1 ==+    BAM_V1_6_BAM_Alignment_OptionalFields_ZOPT bam_v1_6_bam_alignment_optionalfields_zopt_tag2+                                               bam_v1_6_bam_alignment_optionalfields_zopt_value2 =+      bam_v1_6_bam_alignment_optionalfields_zopt_tag1   == bam_v1_6_bam_alignment_optionalfields_zopt_tag2 &&+      bam_v1_6_bam_alignment_optionalfields_zopt_value1 == bam_v1_6_bam_alignment_optionalfields_zopt_value2++instance Show BAM_V1_6_BAM_Alignment_OptionalFields_ZOPT where+  show (BAM_V1_6_BAM_Alignment_OptionalFields_ZOPT tag+                                                   value+       ) =+    "BAM_V1_6_BAM_Alignment_OptionalFields_ZOPT { "          +++    "bam_v1_6_bam_alignment_optionalfields_zopt_tag = "      +++    (show tag)                                               +++    " , bam_v1_6_bam_alignment_optionalfields_zopt_value = " +++    (show value)                                             +++    " }"

@@ -0,0 +1,49 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.BAMAlignments+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.BAMAlignments ( -- * BAM_V1_6_BAM_BAMAlignment version 1.6 data type+                                               BAM_V1_6_BAM_BAMAlignments(..)+                                             ) where++import Data.BAM.Version1_6.BAM.Alignment++import Data.Data+import Data.Sequence+import Generics.Deriving.Base++-- | Custom @"BAM_V1_6_BAM_BAMAlignments"@ (BAM version 1.6) data type.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+newtype BAM_V1_6_BAM_BAMAlignments = BAM_V1_6_BAM_BAMAlignments+  { bam_v1_6_bam_bamalignments_alignments :: Seq BAM_V1_6_BAM_Alignment -- ^ List of alignments.+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_BAMAlignments where+  BAM_V1_6_BAM_BAMAlignments bam_v1_6_bamalignments_alignments1 ==+    BAM_V1_6_BAM_BAMAlignments bam_v1_6_bamalignments_alignments2 =+      bam_v1_6_bamalignments_alignments1 == bam_v1_6_bamalignments_alignments2 ++instance Show BAM_V1_6_BAM_BAMAlignments where+  show (BAM_V1_6_BAM_BAMAlignments alignments+       ) =+    "BAM_V1_6_BAM_BAMAlignments { "        +++    "bam_v1_6_bamalignments_alignments = " +++    (show alignments)                      +++    " }"

@@ -0,0 +1,81 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.BAMHeader+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.BAMHeader ( -- * BAM_V1_6_BAM_BAMHeader version 1.6 data type+                                           BAM_V1_6_BAM_BAMHeader(..)+                                         ) where++import Data.BAM.Version1_6.BAM.ReferenceInformation++import Data.ByteString (ByteString)+import Data.Data+import Data.Sequence+import Data.Word+import Generics.Deriving.Base++-- | Custom @"BAM_V1_6_BAM_BAMHeader"@ (BAM version 1.6) data type.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_BAMHeader = BAM_V1_6_BAM_BAMHeader+  { bam_v1_6_bam_bamheader_magic                 :: ByteString                             -- ^ BAM magic string (magic).+                                                                                           -- This should be BAM\1.+  , bam_v1_6_bam_bamheader_l_text                :: Word32                                 -- ^ Length of the header text, including any NUL padding (l_text).+  , bam_v1_6_bam_bamheader_text                  :: ByteString                             -- ^ Plain header text in SAM;+                                                                                           -- not necessarily NUL-terminated.+  , bam_v1_6_bam_bamheader_n_ref                 :: Word32                                 -- ^ Number of reference sequences (n_ref).+  , bam_v1_6_bam_bamheader_reference_information :: Seq BAM_V1_6_BAM_Reference_Information -- ^ List of reference information (n = bam_v1_6_bam_n_ref).+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_BAMHeader where+  BAM_V1_6_BAM_BAMHeader bam_v1_6_bam_bamheader_magic1+                         bam_v1_6_bam_bamheader_l_text1+                         bam_v1_6_bam_bamheader_text1+                         bam_v1_6_bam_bamheader_n_ref1+                         bam_v1_6_bam_bamheader_reference_information1 ==+    BAM_V1_6_BAM_BAMHeader bam_v1_6_bam_bamheader_magic2+                           bam_v1_6_bam_bamheader_l_text2+                           bam_v1_6_bam_bamheader_text2+                           bam_v1_6_bam_bamheader_n_ref2+                           bam_v1_6_bam_bamheader_reference_information2 =+      bam_v1_6_bam_bamheader_magic1                 == bam_v1_6_bam_bamheader_magic2                         &&+      bam_v1_6_bam_bamheader_l_text1                == bam_v1_6_bam_bamheader_l_text2                        &&+      bam_v1_6_bam_bamheader_text1                  == bam_v1_6_bam_bamheader_text2                          &&+      bam_v1_6_bam_bamheader_n_ref1                 == bam_v1_6_bam_bamheader_n_ref2                         &&+      bam_v1_6_bam_bamheader_reference_information1 == bam_v1_6_bam_bamheader_reference_information2++instance Show BAM_V1_6_BAM_BAMHeader where+  show (BAM_V1_6_BAM_BAMHeader magic+                               l_text+                               text+                               n_ref+                               reference_information+       ) =+    "BAM_V1_6_BAM_BAMHeader { "                          +++    "bam_v1_6_bam_bamheader_magic = "                    +++    (show magic)                                         +++    " , bam_v1_6_bam_bamheader_l_text = "                +++    (show l_text)                                        +++    " , bam_v1_6_bam_bamheader_text = "                  +++    (show text)                                          +++    " , bam_v1_6_bam_bamheader_n_ref = "                 +++    (show n_ref)                                         +++    " , bam_v1_6_bam_bamheader_reference_information = " +++    (show reference_information)                         +++    " }"

@@ -0,0 +1,46 @@+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Header+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Header ( -- * BAM version 1.6 header section data type (RE-EXPORT)+                                        module Data.BAM.Version1_6.BAM.Header.CO,+                                        module Data.BAM.Version1_6.BAM.Header.HD,+                                        module Data.BAM.Version1_6.BAM.Header.PG,+                                        module Data.BAM.Version1_6.BAM.Header.RG,+                                        module Data.BAM.Version1_6.BAM.Header.SQ+                                      ) where++-- | Re-exports.+import Data.BAM.Version1_6.BAM.Header.CO+import Data.BAM.Version1_6.BAM.Header.HD+import Data.BAM.Version1_6.BAM.Header.PG+import Data.BAM.Version1_6.BAM.Header.RG+import Data.BAM.Version1_6.BAM.Header.SQ

@@ -0,0 +1,45 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Header.CO+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Header.CO ( -- * BAM version 1.6 One-line text comment data type+                                           BAM_V1_6_One_Line_Comment(..)+                                         ) where++import Data.ByteString+import Data.Data+import Generics.Deriving.Base++-- | Custom BAM (version 1.6) @"SAM_V1_6_One_Line_Comment"@ data type.+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+newtype BAM_V1_6_One_Line_Comment = BAM_V1_6_One_Line_Comment { bam_v1_6_one_line_comment_value :: ByteString+                                                              }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_One_Line_Comment where+  BAM_V1_6_One_Line_Comment bam_v1_6_one_line_comment_value1 ==+    BAM_V1_6_One_Line_Comment bam_v1_6_one_line_comment_value2 =+      bam_v1_6_one_line_comment_value1 == bam_v1_6_one_line_comment_value2++instance Show BAM_V1_6_One_Line_Comment where+  show (BAM_V1_6_One_Line_Comment value) = "BAM_V1_6_One_Line_Comment { "       +++                                           "bam_v1_6_one_line_comment_value = " +++                                           (show value)                         +++                                           " }"

@@ -0,0 +1,137 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Header.HD+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Header.HD ( -- * BAM version 1.6 File-level metadata data type+                                           BAM_V1_6_File_Level_Metadata(..),+                                           -- * BAM version 1.6 File-Level Metadata data types+                                           BAM_V1_6_File_Level_Metadata_Format_Version(..),+                                           BAM_V1_6_File_Level_Metadata_Sorting_Order(..),+                                           BAM_V1_6_File_Level_Metadata_Alignment_Grouping(..),+                                           BAM_V1_6_File_Level_Metadata_SubSorting_Order(..)+                                         ) where++import Data.ByteString+import Data.Data+import Generics.Deriving.Base++-- | Custom BAM (version 1.6) @"BAM_V1_6_File_Level_Metadata"@ data type.+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_File_Level_Metadata = BAM_V1_6_File_Level_Metadata { bam_v1_6_file_level_metadata_format_version     :: BAM_V1_6_File_Level_Metadata_Format_Version+                                                                 , bam_v1_6_file_level_metadata_sorting_order      :: Maybe BAM_V1_6_File_Level_Metadata_Sorting_Order+                                                                 , bam_v1_6_file_level_metadata_alignment_grouping :: Maybe BAM_V1_6_File_Level_Metadata_Alignment_Grouping+                                                                 , bam_v1_6_file_level_metadata_subsorting_order   :: Maybe BAM_V1_6_File_Level_Metadata_SubSorting_Order+                                                                 }+   deriving (Generic,Typeable)++instance Eq BAM_V1_6_File_Level_Metadata where+  BAM_V1_6_File_Level_Metadata bam_v1_6_file_level_metadata_format_version1+                               bam_v1_6_file_level_metadata_sorting_order1+                               bam_v1_6_file_level_metadata_alignment_grouping1+                               bam_v1_6_file_level_metadata_subsorting_order1 ==+    BAM_V1_6_File_Level_Metadata bam_v1_6_file_level_metadata_format_version2+                                 bam_v1_6_file_level_metadata_sorting_order2+                                 bam_v1_6_file_level_metadata_alignment_grouping2+                                 bam_v1_6_file_level_metadata_subsorting_order2 =+      bam_v1_6_file_level_metadata_format_version1     == bam_v1_6_file_level_metadata_format_version2     &&+      bam_v1_6_file_level_metadata_sorting_order1      == bam_v1_6_file_level_metadata_sorting_order2      &&+      bam_v1_6_file_level_metadata_alignment_grouping1 == bam_v1_6_file_level_metadata_alignment_grouping2 &&+      bam_v1_6_file_level_metadata_subsorting_order1   == bam_v1_6_file_level_metadata_subsorting_order2++instance Show BAM_V1_6_File_Level_Metadata where+  show (BAM_V1_6_File_Level_Metadata version sorting_order alignment_grouping subsorting_order) =+    "BAM_V1_6_File_Level_Metadata { "                       +++    "bam_v1_6_file_level_metadata_format_version = "        +++    (show version)                                          +++    " , bam_v1_6_file_level_metadata_sorting_order = "      +++    (show sorting_order)                                    +++    " , bam_v1_6_file_level_metadata_alignment_grouping = " +++    (show alignment_grouping)                               +++    " , bam_v1_6_file_level_metadata_subsorting_order = "   +++    (show subsorting_order)                                 +++    " }" ++-- | VN tag for @"BAM_V1_6_File_Level_Metadata"@.+newtype BAM_V1_6_File_Level_Metadata_Format_Version = BAM_V1_6_File_Level_Metadata_Format_Version { bam_v1_6_file_level_metadata_format_version_value :: ByteString+                                                                                                  }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_File_Level_Metadata_Format_Version where+  BAM_V1_6_File_Level_Metadata_Format_Version bam_v1_6_file_level_metadata_format_version_value1 ==+    BAM_V1_6_File_Level_Metadata_Format_Version bam_v1_6_file_level_metadata_format_version_value2 =+      bam_v1_6_file_level_metadata_format_version_value1 == bam_v1_6_file_level_metadata_format_version_value2++instance Show BAM_V1_6_File_Level_Metadata_Format_Version where+  show (BAM_V1_6_File_Level_Metadata_Format_Version value) =+    "BAM_V1_6_File_Level_Metadata_Format_Version { "       +++    "bam_v1_6_file_level_metadata_format_version_value = " +++    (show value)                                           +++    " }"++-- | SO tag for @"BAM_V1_6_File_Level_Metadata"@.+newtype BAM_V1_6_File_Level_Metadata_Sorting_Order = BAM_V1_6_File_Level_Metadata_Sorting_Order { bam_v1_6_file_level_metadata_sorting_order_value :: ByteString+                                                                                                }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_File_Level_Metadata_Sorting_Order where+  BAM_V1_6_File_Level_Metadata_Sorting_Order bam_v1_6_file_level_metadata_sorting_order_value1 ==+    BAM_V1_6_File_Level_Metadata_Sorting_Order bam_v1_6_file_level_metadata_sorting_order_value2 =+      bam_v1_6_file_level_metadata_sorting_order_value1 == bam_v1_6_file_level_metadata_sorting_order_value2++instance Show BAM_V1_6_File_Level_Metadata_Sorting_Order where+  show (BAM_V1_6_File_Level_Metadata_Sorting_Order value) =+    "BAM_V1_6_File_Level_Metadata_Sorting_Order { "       +++    "bam_v1_6_file_level_metadata_sorting_order_value = " +++    (show value)                                          +++    " }"++-- | GO tag for @"BAM_V1_6_File_Level_Metadata"@.+newtype BAM_V1_6_File_Level_Metadata_Alignment_Grouping = BAM_V1_6_File_Level_Metadata_Alignment_Grouping { bam_v1_6_file_level_metadata_alignment_grouping_value :: ByteString+                                                                                                          }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_File_Level_Metadata_Alignment_Grouping where+  BAM_V1_6_File_Level_Metadata_Alignment_Grouping bam_v1_6_file_level_metadata_alignment_grouping_value1 ==+    BAM_V1_6_File_Level_Metadata_Alignment_Grouping bam_v1_6_file_level_metadata_alignment_grouping_value2 =+      bam_v1_6_file_level_metadata_alignment_grouping_value1 == bam_v1_6_file_level_metadata_alignment_grouping_value2++instance Show BAM_V1_6_File_Level_Metadata_Alignment_Grouping where+  show (BAM_V1_6_File_Level_Metadata_Alignment_Grouping value) =+    "BAM_V1_6_File_Level_Metadata_Alignment_Grouping { "       +++    "bam_v1_6_file_level_metadata_alignment_grouping_value = " +++    (show value)                                               +++    " }"++-- | SS tag for @"BAM_V1_6_File_Level_Metadata"@.+newtype BAM_V1_6_File_Level_Metadata_SubSorting_Order = BAM_V1_6_File_Level_Metadata_SubSorting_Order { bam_v1_6_file_level_metadata_subsorting_order_value :: ByteString+                                                                                                      }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_File_Level_Metadata_SubSorting_Order where+  BAM_V1_6_File_Level_Metadata_SubSorting_Order bam_v1_6_file_level_metadata_subsorting_order_value1 ==+    BAM_V1_6_File_Level_Metadata_SubSorting_Order bam_v1_6_file_level_metadata_subsorting_order_value2 =+      bam_v1_6_file_level_metadata_subsorting_order_value1 == bam_v1_6_file_level_metadata_subsorting_order_value2++instance Show BAM_V1_6_File_Level_Metadata_SubSorting_Order where+  show (BAM_V1_6_File_Level_Metadata_SubSorting_Order value) =+    "BAM_V1_6_File_Level_Metadata_SubSorting_Order { "       +++    "bam_v1_6_file_level_metadata_subsorting_order_value = " +++    (show value)                                             +++    " }"

@@ -0,0 +1,185 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Header.PG+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Header.PG ( -- * BAM version 1.6 program data type+                                           BAM_V1_6_Program(..),+                                           -- * BAM version 1.6 program data types+                                           BAM_V1_6_Program_Record_Identifier(..),+                                           BAM_V1_6_Program_Name(..),+                                           BAM_V1_6_Program_Command_Line(..),+                                           BAM_V1_6_Program_Previous_PG_ID(..),+                                           BAM_V1_6_Program_Description(..),+                                           BAM_V1_6_Program_Version(..)+                                         ) where++import Data.ByteString+import Data.Data+import Generics.Deriving.Base++-- | Custom BAM (version 1.6) @"BAM_V1_6_Program"@ data type.+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_Program = BAM_V1_6_Program { bam_v1_6_program_record_identifier :: BAM_V1_6_Program_Record_Identifier+                                         , bam_v1_6_program_name              :: Maybe BAM_V1_6_Program_Name+                                         , bam_v1_6_program_command_line      :: Maybe BAM_V1_6_Program_Command_Line+                                         , bam_v1_6_program_previous_pg_id    :: Maybe BAM_V1_6_Program_Previous_PG_ID+                                         , bam_v1_6_program_description       :: Maybe BAM_V1_6_Program_Description+                                         , bam_v1_6_program_version           :: Maybe BAM_V1_6_Program_Version+                                         }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Program where+  BAM_V1_6_Program bam_v1_6_program_record_identifier1+                   bam_v1_6_program_name1+                   bam_v1_6_program_command_line1+                   bam_v1_6_program_previous_pg_id1+                   bam_v1_6_program_description1+                   bam_v1_6_program_version1 ==+    BAM_V1_6_Program bam_v1_6_program_record_identifier2+                     bam_v1_6_program_name2+                     bam_v1_6_program_command_line2+                     bam_v1_6_program_previous_pg_id2+                     bam_v1_6_program_description2+                     bam_v1_6_program_version2 =+      bam_v1_6_program_record_identifier1 == bam_v1_6_program_record_identifier2 &&+      bam_v1_6_program_name1              == bam_v1_6_program_name2              &&+      bam_v1_6_program_command_line1      == bam_v1_6_program_command_line2      &&+      bam_v1_6_program_previous_pg_id1    == bam_v1_6_program_previous_pg_id2    &&+      bam_v1_6_program_description1       == bam_v1_6_program_description2       &&+      bam_v1_6_program_version1           == bam_v1_6_program_version2++instance Show BAM_V1_6_Program where+  show (BAM_V1_6_Program record_identifier name command_line previous_pg_id description version) =+    "BAM_V1_6_Program { "                    +++    "rbam_v1_6_program_record_identifier = " +++    (show record_identifier)                 +++    " , bam_v1_6_program_name = "            +++    (show name)                              +++    " , bam_v1_6_program_command_line = "    +++    (show command_line)                      +++    " , bam_v1_6_program_previous_pg_id = "  +++    (show previous_pg_id)                    +++    " , bam_v1_6_program_description = "     +++    (show description)                       +++    " , bam_v1_6_program_version = "         +++    (show version)                           +++    " }"++-- | ID tag for @"BAM_V1_6_Program"@.+newtype BAM_V1_6_Program_Record_Identifier = BAM_V1_6_Program_Record_Identifier { bam_v1_6_program_record_identifier_value :: ByteString+                                                                                }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Program_Record_Identifier where+  BAM_V1_6_Program_Record_Identifier bam_v1_6_program_record_identifier_value1 ==+    BAM_V1_6_Program_Record_Identifier bam_v1_6_program_record_identifier_value2 =+      bam_v1_6_program_record_identifier_value1 == bam_v1_6_program_record_identifier_value2++instance Show BAM_V1_6_Program_Record_Identifier where+  show (BAM_V1_6_Program_Record_Identifier value) =+    "BAM_V1_6_Program_Record_Identifier { "       +++    "bam_v1_6_program_record_identifier_value = " +++    (show value)                                  +++    " }"++-- | PN tag for @"BAM_V1_6_Program"@.+newtype BAM_V1_6_Program_Name = BAM_V1_6_Program_Name { bam_v1_6_program_name_value :: ByteString+                                                      }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Program_Name where+  BAM_V1_6_Program_Name bam_v1_6_program_name_value1 ==+    BAM_V1_6_Program_Name bam_v1_6_program_name_value2 =+      bam_v1_6_program_name_value1 == bam_v1_6_program_name_value2++instance Show BAM_V1_6_Program_Name where+  show (BAM_V1_6_Program_Name value) =+    "BAM_V1_6_Program_Name { "       +++    "bam_v1_6_program_name_value = " +++    (show value)                     +++    " }"++-- | CL tag for @"BAM_V1_6_Program"@.+newtype BAM_V1_6_Program_Command_Line = BAM_V1_6_Program_Command_Line { bam_v1_6_program_command_line_value :: ByteString+                                                                      }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Program_Command_Line where+  BAM_V1_6_Program_Command_Line bam_v1_6_program_command_line_value1 ==+    BAM_V1_6_Program_Command_Line bam_v1_6_program_command_line_value2 =+      bam_v1_6_program_command_line_value1 == bam_v1_6_program_command_line_value2++instance Show BAM_V1_6_Program_Command_Line where+  show (BAM_V1_6_Program_Command_Line value) =+    "BAM_V1_6_Program_Command_Line { "       +++    "bam_v1_6_program_command_line_value = " +++    (show value)                             +++    " }"++-- | PP tag for @"BAM_V1_6_Program"@.+newtype BAM_V1_6_Program_Previous_PG_ID = BAM_V1_6_Program_Previous_PG_ID { bam_v1_6_program_previous_pg_id_value :: ByteString+                                                                          }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Program_Previous_PG_ID where+  BAM_V1_6_Program_Previous_PG_ID bam_v1_6_program_previous_pg_id_value1 ==+    BAM_V1_6_Program_Previous_PG_ID bam_v1_6_program_previous_pg_id_value2 =+      bam_v1_6_program_previous_pg_id_value1 == bam_v1_6_program_previous_pg_id_value2++instance Show BAM_V1_6_Program_Previous_PG_ID where+  show (BAM_V1_6_Program_Previous_PG_ID value) =+    "BAM_V1_6_Program_Previous_PG_ID { "       +++    "bam_v1_6_program_previous_pg_id_value = " +++    (show value)                               +++    " }"++-- | DS tag for @"BAM_V1_6_Program"@.+newtype BAM_V1_6_Program_Description = BAM_V1_6_Program_Description { bam_v1_6_program_description_value :: ByteString+                                                                    }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Program_Description where+  BAM_V1_6_Program_Description bam_v1_6_program_description_value1 ==+    BAM_V1_6_Program_Description bam_v1_6_program_description_value2 =+      bam_v1_6_program_description_value1 == bam_v1_6_program_description_value2++instance Show BAM_V1_6_Program_Description where+  show (BAM_V1_6_Program_Description value) =+    "BAM_V1_6_Program_Description { "       +++    "bam_v1_6_program_description_value = " +++    (show value)                            +++    " }"++-- | VN tag for @"BAM_V1_6_Program"@.+newtype BAM_V1_6_Program_Version = BAM_V1_6_Program_Version { bam_v1_6_program_version_value :: ByteString+                                                            }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Program_Version where+  BAM_V1_6_Program_Version bam_v1_6_program_version_value1 ==+    BAM_V1_6_Program_Version bam_v1_6_program_version_value2 =+      bam_v1_6_program_version_value1 == bam_v1_6_program_version_value2++instance Show BAM_V1_6_Program_Version where+  show (BAM_V1_6_Program_Version value) =+    "BAM_V1_6_Program_Version { "       +++    "bam_v1_6_program_version_value = " +++    (show value)                        +++    " }"

@@ -0,0 +1,391 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Header.RG+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Header.RG ( -- * BAM version 1.6 Read group data type+                                           BAM_V1_6_Read_Group(..),+                                           -- * BAM version 1.6 Read group data types+                                           BAM_V1_6_Read_Group_Identifier(..),+                                           BAM_V1_6_Read_Group_Barcode_Sequence(..),+                                           BAM_V1_6_Read_Group_Sequencing_Center(..),+                                           BAM_V1_6_Read_Group_Description(..),+                                           BAM_V1_6_Read_Group_Run_Date(..),+                                           BAM_V1_6_Read_Group_Flow_Order(..),+                                           BAM_V1_6_Read_Group_Key_Sequence(..),+                                           BAM_V1_6_Read_Group_Library(..),+                                           BAM_V1_6_Read_Group_Programs(..),+                                           BAM_V1_6_Read_Group_Predicted_Median_Insert_Size(..),+                                           BAM_V1_6_Read_Group_Platform(..),+                                           BAM_V1_6_Read_Group_Platform_Model(..),+                                           BAM_V1_6_Read_Group_Platform_Unit(..),+                                           BAM_V1_6_Read_Group_Sample(..)+                                         ) where++import Data.ByteString+import Data.Data+import Generics.Deriving.Base++-- | Custom BAM (version 1.6) @"BAM_V1_6_Read_Group"@ data type.+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_Read_Group = BAM_V1_6_Read_Group { bam_v1_6_read_group_identifier                   :: BAM_V1_6_Read_Group_Identifier+                                               , bam_v1_6_read_group_barcode_sequence             :: Maybe BAM_V1_6_Read_Group_Barcode_Sequence+                                               , bam_v1_6_read_group_sequencing_center            :: Maybe BAM_V1_6_Read_Group_Sequencing_Center+                                               , bam_v1_6_read_group_description                  :: Maybe BAM_V1_6_Read_Group_Description+                                               , bam_v1_6_read_group_run_date                     :: Maybe BAM_V1_6_Read_Group_Run_Date+                                               , bam_v1_6_read_group_flow_order                   :: Maybe BAM_V1_6_Read_Group_Flow_Order+                                               , bam_v1_6_read_group_key_sequence                 :: Maybe BAM_V1_6_Read_Group_Key_Sequence+                                               , bam_v1_6_read_group_library                      :: Maybe BAM_V1_6_Read_Group_Library+                                               , bam_v1_6_read_group_programs                     :: Maybe BAM_V1_6_Read_Group_Programs+                                               , bam_v1_6_read_group_predicted_median_insert_size :: Maybe BAM_V1_6_Read_Group_Predicted_Median_Insert_Size+                                               , bam_v1_6_read_group_platform                     :: Maybe BAM_V1_6_Read_Group_Platform+                                               , bam_v1_6_read_group_platform_model               :: Maybe BAM_V1_6_Read_Group_Platform_Model+                                               , bam_v1_6_read_group_platform_unit                :: Maybe BAM_V1_6_Read_Group_Platform_Unit+                                               , bam_v1_6_read_group_sample                       :: Maybe BAM_V1_6_Read_Group_Sample+                                               }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Read_Group where+  BAM_V1_6_Read_Group bam_v1_6_read_group_identifier1+                      bam_v1_6_read_group_barcode_sequence1+                      bam_v1_6_read_group_sequencing_center1+                      bam_v1_6_read_group_description1+                      bam_v1_6_read_group_run_date1+                      bam_v1_6_read_group_flow_order1+                      bam_v1_6_read_group_key_sequence1+                      bam_v1_6_read_group_library1+                      bam_v1_6_read_group_programs1+                      bam_v1_6_read_group_predicted_median_insert_size1+                      bam_v1_6_read_group_platform1+                      bam_v1_6_read_group_platform_model1+                      bam_v1_6_read_group_platform_unit1+                      bam_v1_6_read_group_sample1 ==+    BAM_V1_6_Read_Group bam_v1_6_read_group_identifier2+                        bam_v1_6_read_group_barcode_sequence2+                        bam_v1_6_read_group_sequencing_center2+                        bam_v1_6_read_group_description2+                        bam_v1_6_read_group_run_date2+                        bam_v1_6_read_group_flow_order2+                        bam_v1_6_read_group_key_sequence2+                        bam_v1_6_read_group_library2+                        bam_v1_6_read_group_programs2+                        bam_v1_6_read_group_predicted_median_insert_size2+                        bam_v1_6_read_group_platform2+                        bam_v1_6_read_group_platform_model2+                        bam_v1_6_read_group_platform_unit2+                        bam_v1_6_read_group_sample2 =+      bam_v1_6_read_group_identifier1                   == bam_v1_6_read_group_identifier2                   &&+      bam_v1_6_read_group_barcode_sequence1             == bam_v1_6_read_group_barcode_sequence2             &&+      bam_v1_6_read_group_sequencing_center1            == bam_v1_6_read_group_sequencing_center2            &&+      bam_v1_6_read_group_description1                  == bam_v1_6_read_group_description2                  &&+      bam_v1_6_read_group_run_date1                     == bam_v1_6_read_group_run_date2                     &&+      bam_v1_6_read_group_flow_order1                   == bam_v1_6_read_group_flow_order2                   &&+      bam_v1_6_read_group_key_sequence1                 == bam_v1_6_read_group_key_sequence2                 &&+      bam_v1_6_read_group_library1                      == bam_v1_6_read_group_library2                      &&+      bam_v1_6_read_group_programs1                     == bam_v1_6_read_group_programs2                     &&+      bam_v1_6_read_group_predicted_median_insert_size1 == bam_v1_6_read_group_predicted_median_insert_size2 &&+      bam_v1_6_read_group_platform1                     == bam_v1_6_read_group_platform2                     &&+      bam_v1_6_read_group_platform_model1               == bam_v1_6_read_group_platform_model2               &&+      bam_v1_6_read_group_platform_unit1                == bam_v1_6_read_group_platform_unit2                &&+      bam_v1_6_read_group_sample1                       == bam_v1_6_read_group_sample2++instance Show BAM_V1_6_Read_Group where+  show (BAM_V1_6_Read_Group group_identifier+                            barcode_sequence+                            sequencing_center+                            description+                            run_date+                            flow_order+                            key_sequence+                            library+                            programs+                            predicted_median_insert_size+                            platform+                            platform_model+                            platform_unit+                            sample+       ) =+    "BAM_V1_6_Read_Group { "                                      +++    "bam_v1_6_read_group_identifier = "                           +++    (show group_identifier)                                       +++    " , bam_v1_6_read_group_barcode_sequence = "                  +++    (show barcode_sequence)                                       +++    " , bam_v1_6_read_group_sequencing_center = "                 +++    (show sequencing_center)                                      +++    " , bam_v1_6_read_group_description = "                       +++    (show description)                                            +++    " , bam_v1_6_read_group_run_date = "                          +++    (show run_date)                                               +++    " , bam_v1_6_read_group_flow_order = "                        +++    (show flow_order)                                             +++    " , bam_v1_6_read_group_key_sequence = "                      +++    (show key_sequence)                                           +++    " , bam_v1_6_read_group_library = "                           +++    (show library)                                                +++    " , bam_v1_6_read_group_programs = "                          +++    (show programs)                                               +++    " , bam_v1_6_read_group_show_predicted_median_insert_size = " +++    (show predicted_median_insert_size)                           +++    " , bam_v1_6_read_group_platform = "                          +++    (show platform)                                               +++    " , bam_v1_6_read_group_platform_model = "                    +++    (show platform_model)                                         +++    " , bam_v1_6_read_group_platform_unit = "                     +++    (show platform_unit)                                          +++    " , bam_v1_6_read_group_sample = "                            +++    (show sample)                                                 +++    " }"++-- | ID tag for @"BAM_V1_6_Read_Group"@.+newtype BAM_V1_6_Read_Group_Identifier = BAM_V1_6_Read_Group_Identifier { bam_v1_6_read_group_identifier_value :: ByteString+                                                                        }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Read_Group_Identifier where+  BAM_V1_6_Read_Group_Identifier bam_v1_6_read_group_identifier_value1 ==+    BAM_V1_6_Read_Group_Identifier bam_v1_6_read_group_identifier_value2 =+      bam_v1_6_read_group_identifier_value1 == bam_v1_6_read_group_identifier_value2++instance Show BAM_V1_6_Read_Group_Identifier where+  show (BAM_V1_6_Read_Group_Identifier value) =+    "BAM_V1_6_Read_Group_Identifier { "       +++    "bam_v1_6_read_group_identifier_value = " +++    (show value)                              +++    " }"++-- | BC tag for @"BAM_V1_6_Read_Group"@.+newtype BAM_V1_6_Read_Group_Barcode_Sequence = BAM_V1_6_Read_Group_Barcode_Sequence { bam_v1_6_read_group_barcode_sequence_value :: ByteString+                                                                                    }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Read_Group_Barcode_Sequence where+  BAM_V1_6_Read_Group_Barcode_Sequence bam_v1_6_read_group_barcode_sequence_value1 ==+    BAM_V1_6_Read_Group_Barcode_Sequence bam_v1_6_read_group_barcode_sequence_value2 =+      bam_v1_6_read_group_barcode_sequence_value1 == bam_v1_6_read_group_barcode_sequence_value2++instance Show BAM_V1_6_Read_Group_Barcode_Sequence where+  show (BAM_V1_6_Read_Group_Barcode_Sequence value) =+    "BAM_V1_6_Read_Group_Barcode_Sequence { "       +++    "bam_v1_6_read_group_barcode_sequence_value = " +++    (show value)                                    +++    " }"++-- | CN tag for @"BAM_V1_6_Read_Group"@.+newtype BAM_V1_6_Read_Group_Sequencing_Center = BAM_V1_6_Read_Group_Sequencing_Center { bam_v1_6_read_group_sequencing_center_value :: ByteString+                                                                                      }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Read_Group_Sequencing_Center where+  BAM_V1_6_Read_Group_Sequencing_Center bam_v1_6_read_group_sequencing_center_value1 ==+    BAM_V1_6_Read_Group_Sequencing_Center bam_v1_6_read_group_sequencing_center_value2 =+      bam_v1_6_read_group_sequencing_center_value1 == bam_v1_6_read_group_sequencing_center_value2++instance Show BAM_V1_6_Read_Group_Sequencing_Center where+  show (BAM_V1_6_Read_Group_Sequencing_Center value) =+    "BAM_V1_6_Read_Group_Sequencing_Center { "       +++    "bam_v1_6_read_group_sequencing_center_value = " +++    (show value)                                     +++    " }"++-- | DS tag for @"BAM_V1_6_Read_Group"@.+newtype BAM_V1_6_Read_Group_Description = BAM_V1_6_Read_Group_Description { bam_v1_6_read_group_description_value :: ByteString+                                                                          }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Read_Group_Description where+  BAM_V1_6_Read_Group_Description bam_v1_6_read_group_description_value1 ==+    BAM_V1_6_Read_Group_Description bam_v1_6_read_group_description_value2 =+      bam_v1_6_read_group_description_value1 == bam_v1_6_read_group_description_value2++instance Show BAM_V1_6_Read_Group_Description where+  show (BAM_V1_6_Read_Group_Description value) =+    "BAM_V1_6_Read_Group_Description { "       +++    "bam_v1_6_read_group_description_value = " +++    (show value)                               +++    " }"++-- | DT tag for @"BAM_V1_6_Read_Group"@.+newtype BAM_V1_6_Read_Group_Run_Date = BAM_V1_6_Read_Group_Run_Date { bam_v1_6_read_group_run_date_value :: ByteString+                                                                    }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Read_Group_Run_Date where+  BAM_V1_6_Read_Group_Run_Date bam_v1_6_read_group_run_date_value1 ==+    BAM_V1_6_Read_Group_Run_Date bam_v1_6_read_group_run_date_value2 =+      bam_v1_6_read_group_run_date_value1 == bam_v1_6_read_group_run_date_value2++instance Show BAM_V1_6_Read_Group_Run_Date where+  show (BAM_V1_6_Read_Group_Run_Date value) =+    "BAM_V1_6_Read_Group_Run_Date { "       +++    "bam_v1_6_read_group_run_date_value = " +++    (show value)                            +++    " }"++-- | FO tag for @"BAM_V1_6_Read_Group"@.+newtype BAM_V1_6_Read_Group_Flow_Order = BAM_V1_6_Read_Group_Flow_Order { bam_v1_6_read_group_flow_order_value :: ByteString+                                                                        }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Read_Group_Flow_Order where+  BAM_V1_6_Read_Group_Flow_Order bam_v1_6_one_line_comment_value1 ==+    BAM_V1_6_Read_Group_Flow_Order bam_v1_6_read_group_flow_order_value2 =+      bam_v1_6_one_line_comment_value1 == bam_v1_6_read_group_flow_order_value2++instance Show BAM_V1_6_Read_Group_Flow_Order where+  show (BAM_V1_6_Read_Group_Flow_Order value) =+    "BAM_V1_6_Read_Group_Flow_Order { "       +++    "bam_v1_6_read_group_flow_order_value = " +++    (show value)                              +++    " }"++-- | KS tag for @"BAM_V1_6_Read_Group"@.+newtype BAM_V1_6_Read_Group_Key_Sequence = BAM_V1_6_Read_Group_Key_Sequence { bam_v1_6_read_group_key_sequence_value :: ByteString+                                                                            }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Read_Group_Key_Sequence where+  BAM_V1_6_Read_Group_Key_Sequence bam_v1_6_read_group_key_sequence_value1 ==+    BAM_V1_6_Read_Group_Key_Sequence bam_v1_6_read_group_key_sequence_value2 =+      bam_v1_6_read_group_key_sequence_value1 == bam_v1_6_read_group_key_sequence_value2++instance Show BAM_V1_6_Read_Group_Key_Sequence where+  show (BAM_V1_6_Read_Group_Key_Sequence value) =+    "BAM_V1_6_Read_Group_Key_Sequence { "       +++    "bam_v1_6_read_group_key_sequence_value = " +++    (show value)                                +++    " }"++-- | LB tag for @"BAM_V1_6_Read_Group"@.+newtype BAM_V1_6_Read_Group_Library = BAM_V1_6_Read_Group_Library { bam_v1_6_read_group_library_value :: ByteString+                                                                  }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Read_Group_Library where+  BAM_V1_6_Read_Group_Library bam_v1_6_read_group_library_value1 ==+    BAM_V1_6_Read_Group_Library bam_v1_6_read_group_library_value2 =+      bam_v1_6_read_group_library_value1 == bam_v1_6_read_group_library_value2++instance Show BAM_V1_6_Read_Group_Library where+  show (BAM_V1_6_Read_Group_Library value) =+    "BAM_V1_6_Read_Group_Library { "       +++    "bam_v1_6_read_group_library_value = " +++    (show value)                           +++    " }"++-- | PG tag for @"BAM_V1_6_Read_Group"@.+newtype BAM_V1_6_Read_Group_Programs = BAM_V1_6_Read_Group_Programs { bam_v1_6_read_group_programs_value :: ByteString+                                                                    }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Read_Group_Programs where+  BAM_V1_6_Read_Group_Programs bam_v1_6_read_group_programs_value1 ==+    BAM_V1_6_Read_Group_Programs bam_v1_6_read_group_programs_value2 =+      bam_v1_6_read_group_programs_value1 == bam_v1_6_read_group_programs_value2++instance Show BAM_V1_6_Read_Group_Programs where+  show (BAM_V1_6_Read_Group_Programs value) =+    "BAM_V1_6_Read_Group_Programs { "       +++    "bam_v1_6_read_group_programs_value = " +++    (show value)                            +++    " }"++-- | PI tag for @"BAM_V1_6_Read_Group"@.+newtype BAM_V1_6_Read_Group_Predicted_Median_Insert_Size = BAM_V1_6_Read_Group_Predicted_Median_Insert_Size { bam_v1_6_read_group_predicted_median_insert_size_value :: ByteString+                                                                                                            }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Read_Group_Predicted_Median_Insert_Size where+  BAM_V1_6_Read_Group_Predicted_Median_Insert_Size bam_v1_6_read_group_predicted_median_insert_size_value1 ==+    BAM_V1_6_Read_Group_Predicted_Median_Insert_Size bam_v1_6_read_group_predicted_median_insert_size_value2 =+      bam_v1_6_read_group_predicted_median_insert_size_value1 == bam_v1_6_read_group_predicted_median_insert_size_value2++instance Show BAM_V1_6_Read_Group_Predicted_Median_Insert_Size where+  show (BAM_V1_6_Read_Group_Predicted_Median_Insert_Size value) =+    "BAM_V1_6_Read_Group_Predicted_Median_Insert_Size { "       +++    "bam_v1_6_read_group_predicted_median_insert_size_value = " +++    (show value)                                                +++    " }"++-- | PL tag for @"BAM_V1_6_Read_Group"@.+newtype BAM_V1_6_Read_Group_Platform = BAM_V1_6_Read_Group_Platform { bam_v1_6_read_group_platform_value :: ByteString+                                                                    }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Read_Group_Platform where+  BAM_V1_6_Read_Group_Platform bam_v1_6_read_group_platform_value1 ==+    BAM_V1_6_Read_Group_Platform bam_v1_6_read_group_platform_value2 =+      bam_v1_6_read_group_platform_value1 == bam_v1_6_read_group_platform_value2++instance Show BAM_V1_6_Read_Group_Platform where+  show (BAM_V1_6_Read_Group_Platform value) =+    "BAM_V1_6_Read_Group_Platform { "       +++    "bam_v1_6_read_group_platform_value = " +++    (show value)                            +++    " }"++-- | PM tag for @"BAM_V1_6_Read_Group"@.+newtype BAM_V1_6_Read_Group_Platform_Model = BAM_V1_6_Read_Group_Platform_Model { bam_v1_6_read_group_platform_model_value :: ByteString+                                                                                }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Read_Group_Platform_Model where+  BAM_V1_6_Read_Group_Platform_Model bam_v1_6_read_group_platform_model_value1 ==+    BAM_V1_6_Read_Group_Platform_Model bam_v1_6_read_group_platform_model_value2 =+      bam_v1_6_read_group_platform_model_value1 == bam_v1_6_read_group_platform_model_value2++instance Show BAM_V1_6_Read_Group_Platform_Model where+  show (BAM_V1_6_Read_Group_Platform_Model value) =+    "BAM_V1_6_Read_Group_Platform_Model { "       +++    "bam_v1_6_read_group_platform_model_value = " +++    (show value)                                  +++    " }"++-- | PU tag for @"BAM_V1_6_Read_Group"@.+newtype BAM_V1_6_Read_Group_Platform_Unit = BAM_V1_6_Read_Group_Platform_Unit { bam_v1_6_read_group_platform_unit_value :: ByteString+                                                                              }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Read_Group_Platform_Unit where+  BAM_V1_6_Read_Group_Platform_Unit bam_v1_6_read_group_platform_unit_value1 ==+    BAM_V1_6_Read_Group_Platform_Unit bam_v1_6_read_group_platform_unit_value2 =+      bam_v1_6_read_group_platform_unit_value1 == bam_v1_6_read_group_platform_unit_value2++instance Show BAM_V1_6_Read_Group_Platform_Unit where+  show (BAM_V1_6_Read_Group_Platform_Unit value) =+    "BAM_V1_6_Read_Group_Platform_Unit { "       +++    "bam_v1_6_read_group_platform_unit_value = " +++    (show value)                                 +++    " }"++-- | SM tag for @"BAM_V1_6_Read_Group"@.+newtype BAM_V1_6_Read_Group_Sample = BAM_V1_6_Read_Group_Sample { bam_v1_6_read_group_sample_value :: ByteString+                                                                }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Read_Group_Sample where+  BAM_V1_6_Read_Group_Sample bam_v1_6_read_group_sample_value1 ==+    BAM_V1_6_Read_Group_Sample bam_v1_6_read_group_sample_value2 =+      bam_v1_6_read_group_sample_value1 == bam_v1_6_read_group_sample_value2++instance Show BAM_V1_6_Read_Group_Sample where+  show (BAM_V1_6_Read_Group_Sample value) =+    "BAM_V1_6_Read_Group_Sample { "       +++    "bam_v1_6_read_group_sample_value = " +++    (show value)                          +++    " }"

@@ -0,0 +1,291 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.Header.SQ+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.Header.SQ ( -- * BAM version 1.6 Reference sequence dictionary data type+                                           BAM_V1_6_Reference_Sequence_Dictionary(..),+                                           -- * BAM version 1.6 Reference sequence dictionary data types+                                           BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name(..),+                                           BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length(..),+                                           BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus(..),+                                           BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names(..),+                                           BAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier(..),+                                           BAM_V1_6_Reference_Sequence_Dictionary_Description(..),+                                           BAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum(..),+                                           BAM_V1_6_Reference_Sequence_Dictionary_Species(..),+                                           BAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology(..),+                                           BAM_V1_6_Reference_Sequence_Dictionary_URI(..)+                                         ) where++import Data.ByteString+import Data.Data+import Generics.Deriving.Base++-- | Custom BAM (version 1.6) @"BAM_V1_6_Reference_Sequence_Dictionary"@ data type.+--+-- See section 4.2 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_Reference_Sequence_Dictionary = BAM_V1_6_Reference_Sequence_Dictionary { bam_v1_6_reference_sequence_dictionary_reference_sequence_name                        :: BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name+                                                                                     , bam_v1_6_reference_sequence_dictionary_reference_sequence_length                      :: BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length+                                                                                     , bam_v1_6_reference_sequence_dictionary_alternative_locus                              :: Maybe BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus+                                                                                     , bam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names           :: Maybe BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names+                                                                                     , bam_v1_6_reference_sequence_dictionary_genome_assembly_identifier                     :: Maybe BAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier+                                                                                     , bam_v1_6_reference_sequence_dictionary_description                                    :: Maybe BAM_V1_6_Reference_Sequence_Dictionary_Description+                                                                                     , bam_v1_6_reference_sequence_dictionary_md5_checksum                                   :: Maybe BAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum+                                                                                     , bam_v1_6_reference_sequence_dictionary_species                                        :: Maybe BAM_V1_6_Reference_Sequence_Dictionary_Species+                                                                                     , bam_v1_6_reference_sequence_dictionary_molecule_topology                              :: Maybe BAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology                                       +                                                                                     , bam_v1_6_reference_sequence_dictionary_uri                                            :: Maybe BAM_V1_6_Reference_Sequence_Dictionary_URI +                                                                                     }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Reference_Sequence_Dictionary where+  BAM_V1_6_Reference_Sequence_Dictionary bam_v1_6_reference_sequence_dictionary_reference_sequence_name1+                                         bam_v1_6_reference_sequence_dictionary_reference_sequence_length1+                                         bam_v1_6_reference_sequence_dictionary_reference_alternative_locus1+                                         bam_v1_6_reference_sequence_dictionary_reference_alternative_reference_sequence_names1+                                         bam_v1_6_reference_sequence_dictionary_genome_assembly_identifier1+                                         bam_v1_6_reference_sequence_dictionary_description1+                                         bam_v1_6_reference_sequence_dictionary_md5_checksum1+                                         bam_v1_6_reference_sequence_dictionary_species1+                                         bam_v1_6_reference_sequence_dictionary_molecule_topology1+                                         bam_v1_6_reference_sequence_dictionary_uri1 ==+    BAM_V1_6_Reference_Sequence_Dictionary bam_v1_6_reference_sequence_dictionary_reference_sequence_name2+                                           bam_v1_6_reference_sequence_dictionary_reference_sequence_length2+                                           bam_v1_6_reference_sequence_dictionary_reference_alternative_locus2+                                           bam_v1_6_reference_sequence_dictionary_reference_alternative_reference_sequence_names2+                                           bam_v1_6_reference_sequence_dictionary_genome_assembly_identifier2+                                           bam_v1_6_reference_sequence_dictionary_description2+                                           bam_v1_6_reference_sequence_dictionary_md5_checksum2+                                           bam_v1_6_reference_sequence_dictionary_species2+                                           bam_v1_6_reference_sequence_dictionary_molecule_topology2+                                           bam_v1_6_reference_sequence_dictionary_uri2 =+      bam_v1_6_reference_sequence_dictionary_reference_sequence_name1                        == bam_v1_6_reference_sequence_dictionary_reference_sequence_name2                        &&+      bam_v1_6_reference_sequence_dictionary_reference_sequence_length1                      == bam_v1_6_reference_sequence_dictionary_reference_sequence_length2                      &&+      bam_v1_6_reference_sequence_dictionary_reference_alternative_locus1                    == bam_v1_6_reference_sequence_dictionary_reference_alternative_locus2                    &&+      bam_v1_6_reference_sequence_dictionary_reference_alternative_reference_sequence_names1 == bam_v1_6_reference_sequence_dictionary_reference_alternative_reference_sequence_names2 &&+      bam_v1_6_reference_sequence_dictionary_genome_assembly_identifier1                     == bam_v1_6_reference_sequence_dictionary_genome_assembly_identifier2                     &&+      bam_v1_6_reference_sequence_dictionary_description1                                    == bam_v1_6_reference_sequence_dictionary_description2                                    &&+      bam_v1_6_reference_sequence_dictionary_md5_checksum1                                   == bam_v1_6_reference_sequence_dictionary_md5_checksum2                                   &&+      bam_v1_6_reference_sequence_dictionary_species1                                        == bam_v1_6_reference_sequence_dictionary_species2                                        &&+      bam_v1_6_reference_sequence_dictionary_molecule_topology1                              == bam_v1_6_reference_sequence_dictionary_molecule_topology2                              &&+      bam_v1_6_reference_sequence_dictionary_uri1                                            == bam_v1_6_reference_sequence_dictionary_uri2++instance Show BAM_V1_6_Reference_Sequence_Dictionary where+  show (BAM_V1_6_Reference_Sequence_Dictionary reference_sequence_name+                                               reference_sequence_length+                                               reference_alternative_locus+                                               reference_alternative_sequence_names+                                               genome_assembly_identifier+                                               description+                                               md5_checksum+                                               species+                                               molecule_topology+                                               uri+       ) =+    "BAM_V1_6_Reference_Sequence_Dictionary { "                                         +++    "bam_v1_6_reference_sequence_dictionary_reference_sequence_name = "                 +++    (show reference_sequence_name)                                                      +++    " , bam_v1_6_reference_sequence_dictionary_reference_sequence_length = "            +++    (show reference_sequence_length)                                                    +++    " , bam_v1_6_reference_sequence_dictionary_alternative_locus = "                    +++    (show reference_alternative_locus)                                                  +++    " , bam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names = " +++    (show reference_alternative_sequence_names)                                         +++    " , bam_v1_6_reference_sequence_dictionary_genome_assembly_identifier = "           +++    (show genome_assembly_identifier)                                                   +++    " , bam_v1_6_reference_sequence_dictionary_description = "                          +++    (show description)                                                                  +++    " , bam_v1_6_reference_sequence_dictionary_md5_checksum = "                         +++    (show md5_checksum)                                                                 +++    " , bam_v1_6_reference_sequence_dictionary_species = "                              +++    (show species)                                                                      +++    " , bam_v1_6_reference_sequence_dictionary_molecule_topology = "                    +++    (show molecule_topology)                                                            +++    " , bam_v1_6_reference_sequence_dictionary_uri = "                                  +++    (show uri)                                                                          +++    " }"++-- | SN tag for @"BAM_V1_6_Reference_Sequence_Dictionary"@.+newtype BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name = BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name { bam_v1_6_reference_sequence_dictionary_reference_sequence_name_value :: ByteString +                                                                                                                                        }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name where+  BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name bam_v1_6_reference_sequence_dictionary_reference_sequence_name_value1 ==+    BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name bam_v1_6_reference_sequence_dictionary_reference_sequence_name_value2 =+      bam_v1_6_reference_sequence_dictionary_reference_sequence_name_value1 == bam_v1_6_reference_sequence_dictionary_reference_sequence_name_value2  ++instance Show BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name where+  show (BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name value) =+    "BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name { "       +++    "bam_v1_6_reference_sequence_dictionary_reference_sequence_name_value = " +++    (show value)                                                              +++    " }"++-- | LN tag for @"BAM_V1_6_Reference_Sequence_Dictionary"@.+newtype BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length = BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length { bam_v1_6_reference_sequence_dictionary_reference_sequence_length_value :: ByteString+                                                                                                                                            }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length where+  BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length bam_v1_6_reference_sequence_dictionary_reference_sequence_length_value1 ==+    BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length bam_v1_6_reference_sequence_dictionary_reference_sequence_length_value2 =+      bam_v1_6_reference_sequence_dictionary_reference_sequence_length_value1 == bam_v1_6_reference_sequence_dictionary_reference_sequence_length_value2++instance Show BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length where+  show (BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length value) =+    "BAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length { "       +++    "bam_v1_6_reference_sequence_dictionary_reference_sequence_length_value = " +++    (show value)                                                                +++    " }"++-- | AH tag for @"BAM_V1_6_Reference_Sequence_Dictionary"@.+newtype BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus = BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus { bam_v1_6_reference_sequence_dictionary_alternative_locus_value :: ByteString+                                                                                                                            }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus where+  BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus bam_v1_6_reference_sequence_dictionary_alternative_locus_value1 ==+    BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus bam_v1_6_reference_sequence_dictionary_alternative_locus_value2 =+      bam_v1_6_reference_sequence_dictionary_alternative_locus_value1 == bam_v1_6_reference_sequence_dictionary_alternative_locus_value2++instance Show BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus where+  show (BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus value) =+    "BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus { "       +++    "bam_v1_6_reference_sequence_dictionary_alternative_locus_value = " +++    (show value)                                                        +++    " }"++-- | AN tag for @"BAM_V1_6_Reference_Sequence_Dictionary"@.+newtype BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names = BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names { bam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value :: ByteString+                                                                                                                                                                  }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names where+  BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names bam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value1 ==+    BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names bam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value2 =+      bam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value1 == bam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value2++instance Show BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names where+  show (BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names value) =+    "BAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names { "       +++    "bam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value = " +++    (show value)                                                                           +++    " }"++-- | AS tag for @"BAM_V1_6_Reference_Sequence_Dictionary"@.+newtype BAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier = BAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier { bam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value :: ByteString+                                                                                                                                              }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier where+  BAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier bam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value1 ==+    BAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier bam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value2 =+      bam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value1 == bam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value2++instance Show BAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier where+  show (BAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier value) =+    "BAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier { "       +++    "bam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value = " +++    (show value)                                                                 +++    " }"++-- | DS tag for @"BAM_V1_6_Reference_Sequence_Dictionary"@.+newtype BAM_V1_6_Reference_Sequence_Dictionary_Description = BAM_V1_6_Reference_Sequence_Dictionary_Description { bam_v1_6_reference_sequence_dictionary_description_value :: ByteString+                                                                                                                }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Reference_Sequence_Dictionary_Description where+  BAM_V1_6_Reference_Sequence_Dictionary_Description bam_v1_6_reference_sequence_dictionary_description_value1 ==+    BAM_V1_6_Reference_Sequence_Dictionary_Description bam_v1_6_reference_sequence_dictionary_description_value2 =+      bam_v1_6_reference_sequence_dictionary_description_value1 == bam_v1_6_reference_sequence_dictionary_description_value2++instance Show BAM_V1_6_Reference_Sequence_Dictionary_Description where+  show (BAM_V1_6_Reference_Sequence_Dictionary_Description value) =+    "BAM_V1_6_Reference_Sequence_Dictionary_Description { "       +++    "bam_v1_6_reference_sequence_dictionary_description_value = " +++    (show value)                                                  +++    " }"++-- | M5 tag for @"BAM_V1_6_Reference_Sequence_Dictionary"@.+newtype BAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum = BAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum { bam_v1_6_reference_sequence_dictionary_md5_checksum_value :: ByteString+                                                                                                                  }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum where+  BAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum bam_v1_6_reference_sequence_dictionary_md5_checksum_value1 ==+    BAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum bam_v1_6_reference_sequence_dictionary_md5_checksum_value2 =+      bam_v1_6_reference_sequence_dictionary_md5_checksum_value1 == bam_v1_6_reference_sequence_dictionary_md5_checksum_value2++instance Show BAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum where+  show (BAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum value) =+    "BAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum { "       +++    "bam_v1_6_reference_sequence_dictionary_md5_checksum_value = " +++    (show value)                                                   +++    " }"++-- | SP tag for @"BAM_V1_6_Reference_Sequence_Dictionary"@.+newtype BAM_V1_6_Reference_Sequence_Dictionary_Species = BAM_V1_6_Reference_Sequence_Dictionary_Species { bam_v1_6_reference_sequence_dictionary_species_value :: ByteString+                                                                                                        }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Reference_Sequence_Dictionary_Species where+  BAM_V1_6_Reference_Sequence_Dictionary_Species bam_v1_6_reference_sequence_dictionary_species_value1 ==+    BAM_V1_6_Reference_Sequence_Dictionary_Species bam_v1_6_reference_sequence_dictionary_species_value2 =+      bam_v1_6_reference_sequence_dictionary_species_value1 == bam_v1_6_reference_sequence_dictionary_species_value2++instance Show BAM_V1_6_Reference_Sequence_Dictionary_Species where+  show (BAM_V1_6_Reference_Sequence_Dictionary_Species value) =+    "BAM_V1_6_Reference_Sequence_Dictionary_Species { "       +++    "bam_v1_6_reference_sequence_dictionary_species_value = " +++    (show value)                                              +++    " }"++-- | TP tag for @"BAM_V1_6_Reference_Sequence_Dictionary"@.+newtype BAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology = BAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology { bam_v1_6_reference_sequence_dictionary_molecule_topology_value :: ByteString+                                                                                                                            }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology where+  BAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology bam_v1_6_reference_sequence_dictionary_molecule_topology_value1 ==+    BAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology bam_v1_6_reference_sequence_dictionary_molecule_topology_value2 =+      bam_v1_6_reference_sequence_dictionary_molecule_topology_value1 == bam_v1_6_reference_sequence_dictionary_molecule_topology_value2++instance Show BAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology where+  show (BAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology value) =+    "BAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology { "       +++    "bam_v1_6_reference_sequence_dictionary_molecule_topology_value = " +++    (show value)                                                        +++    " }"++-- | UR tag for @"BAM_V1_6_Reference_Sequence_Dictionary"@.+newtype BAM_V1_6_Reference_Sequence_Dictionary_URI = BAM_V1_6_Reference_Sequence_Dictionary_URI { bam_v1_6_reference_sequence_dictionary_uri_value :: ByteString+                                                                                                }+  deriving (Generic,Typeable)++instance Eq BAM_V1_6_Reference_Sequence_Dictionary_URI where+  BAM_V1_6_Reference_Sequence_Dictionary_URI bam_v1_6_reference_sequence_dictionary_uri_value1 ==+    BAM_V1_6_Reference_Sequence_Dictionary_URI bam_v1_6_reference_sequence_dictionary_uri_value2 =+      bam_v1_6_reference_sequence_dictionary_uri_value1 == bam_v1_6_reference_sequence_dictionary_uri_value2++instance Show BAM_V1_6_Reference_Sequence_Dictionary_URI where+  show (BAM_V1_6_Reference_Sequence_Dictionary_URI value) =+    "BAM_V1_6_Reference_Sequence_Dictionary_URI { "       +++    "bam_v1_6_reference_sequence_dictionary_uri_value = " +++    (show value)                                          +++    " }"

@@ -0,0 +1,38 @@+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.ReferenceInformation+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.ReferenceInformation ( -- * BAM version 1.6 reference information mandatory and optional data types (RE-EXPORT)+                                                      module Data.BAM.Version1_6.BAM.ReferenceInformation.Base+                                                    ) where++-- | Re-exports.+import Data.BAM.Version1_6.BAM.ReferenceInformation.Base

@@ -0,0 +1,62 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BAM.ReferenceInformation.Base+-- Copyright   :  (c) Matthew Mosior 2023+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BAM.ReferenceInformation.Base ( -- * BAM_V1_6_BAM_Reference_Information version 1.6 data type+                                                           BAM_V1_6_BAM_Reference_Information(..)+                                                         ) where++import Data.ByteString+import Data.Data+import Data.Word+import Generics.Deriving.Base++-- | Custom @"BAM_V1_6_BAM_Reference_Information"@ (BAM version 1.6) data type.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BAM_Reference_Information = BAM_V1_6_BAM_Reference_Information+  { bam_v1_6_bam_reference_information_l_name :: Word32     -- ^ Length of the reference name plus 1 (including NUL).+  , bam_v1_6_bam_reference_information_name   :: ByteString -- ^ Reference sequence name; NUL terminated.+  , bam_v1_6_bam_reference_information_l_ref  :: Word32     -- ^ Length of the reference sequence.+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BAM_Reference_Information where+  BAM_V1_6_BAM_Reference_Information bam_v1_6_bam_reference_information_l_name1+                                     bam_v1_6_bam_reference_information_name1+                                     bam_v1_6_bam_reference_information_l_ref1 ==+    BAM_V1_6_BAM_Reference_Information bam_v1_6_bam_reference_information_l_name2+                                       bam_v1_6_bam_reference_information_name2+                                       bam_v1_6_bam_reference_information_l_ref2 =+      bam_v1_6_bam_reference_information_l_name1 == bam_v1_6_bam_reference_information_l_name2 &&+      bam_v1_6_bam_reference_information_name1   == bam_v1_6_bam_reference_information_name2   &&+      bam_v1_6_bam_reference_information_l_ref1  == bam_v1_6_bam_reference_information_l_ref2++instance Show BAM_V1_6_BAM_Reference_Information where+  show (BAM_V1_6_BAM_Reference_Information l_name+                                           name+                                           l_ref+       ) =+    "BAM_V1_6_BAM_Reference_Information { "          +++    "bam_v1_6_bam_reference_information_l_name = "   +++    (show l_name)                                    +++    " , bam_v1_6_bam_reference_information_name = "  +++    (show name)                                      +++    " , bam_v1_6_bam_reference_information_l_ref = " +++    (show l_ref)                                     +++    " }"

@@ -0,0 +1,112 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.BGZFBlock+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.BGZFBlock ( -- * BAM_V1_6_BGZFBlock version 1.6 data type+                                       BAM_V1_6_BGZFBlock(..)+                                     ) where++import Data.BAM.Version1_6.BAM+import Data.BAM.Version1_6.GZipHeader++import Data.Data+import Data.Word+import Generics.Deriving.Base++-- | Custom @"BAM_V1_6_BGZFBlock"@ (BAM version 1.6) data type.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_BGZFBlock = BAM_V1_6_BGZFBlock+  { bam_v1_6_bgzfblock_gzip_header                :: BAM_V1_6_GZipHeader -- ^ GZip 10 byte header.+                                                                         -- This contains a magic number (1f 08),+                                                                         -- the compression method (08 for DEFLATE),+                                                                         -- 1-byte of header flags,+                                                                         -- a 4-byte timestamp,+                                                                         -- compression flags,+                                                                         -- and the operating system ID.+  , bam_v1_6_bgzfblock_subfield_identifier_one    :: Word8               -- ^ This should be 'B'.+  , bam_v1_6_bgzfblock_subfield_identifier_two    :: Word8               -- ^ This should be 'C'.+  , bam_v1_6_bgzfblock_subfield_length            :: Word16              -- ^ This should be '02 00'.+  , bam_v1_6_bgzfblock_total_block_size_minus_one :: Word16              -- ^ The payload of the BGZF+                                                                         -- extra field is a 16-bit unsigned+                                                                         -- integer in little endian format.+                                                                         -- This integer gives the size of the+                                                                         -- containing BGZF block minus one.+  , bam_v1_6_bgzfblock_cdata                      :: BAM_V1_6_BAM        -- ^ Compressed DATA by zlib::deflate().+                                                                         -- The data in this field will be+                                                                         -- in a decompressed and+                                                                         -- useable state.+  , bam_v1_6_bgzfblock_crc32                      :: Word32              -- ^ CRC-32.+  , bam_v1_6_bgzfblock_isize                      :: Word32              -- ^ Input SIZE (length of uncompressed data).+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_BGZFBlock where+  BAM_V1_6_BGZFBlock bam_v1_6_bgzfblock_gzip_header1+                     bam_v1_6_bgzfblock_subfield_identifier_one1+                     bam_v1_6_bgzfblock_subfield_identifier_two1+                     bam_v1_6_bgzfblock_subfield_length1+                     bam_v1_6_bgzfblock_total_block_size_minus_one1+                     bam_v1_6_bgzfblock_cdata1+                     bam_v1_6_bgzfblock_crc321+                     bam_v1_6_bgzfblock_isize1 ==+    BAM_V1_6_BGZFBlock bam_v1_6_bgzfblock_gzip_header2+                       bam_v1_6_bgzfblock_subfield_identifier_one2+                       bam_v1_6_bgzfblock_subfield_identifier_two2+                       bam_v1_6_bgzfblock_subfield_length2+                       bam_v1_6_bgzfblock_total_block_size_minus_one2+                       bam_v1_6_bgzfblock_cdata2+                       bam_v1_6_bgzfblock_crc322+                       bam_v1_6_bgzfblock_isize2 =+      bam_v1_6_bgzfblock_gzip_header1                == bam_v1_6_bgzfblock_gzip_header2                &&+      bam_v1_6_bgzfblock_subfield_identifier_one1    == bam_v1_6_bgzfblock_subfield_identifier_one2    &&+      bam_v1_6_bgzfblock_subfield_identifier_two1    == bam_v1_6_bgzfblock_subfield_identifier_two2    &&+      bam_v1_6_bgzfblock_subfield_length1            == bam_v1_6_bgzfblock_subfield_length2            &&+      bam_v1_6_bgzfblock_total_block_size_minus_one1 == bam_v1_6_bgzfblock_total_block_size_minus_one2 &&+      bam_v1_6_bgzfblock_cdata1                      == bam_v1_6_bgzfblock_cdata2                      &&+      bam_v1_6_bgzfblock_crc321                      == bam_v1_6_bgzfblock_crc322                      &&+      bam_v1_6_bgzfblock_isize1                      == bam_v1_6_bgzfblock_isize2++instance Show BAM_V1_6_BGZFBlock where+  show (BAM_V1_6_BGZFBlock gzip_header+                           subfield_identifier_one+                           subfield_identifier_two+                           subfield_length+                           total_block_size_minus_one+                           cdata+                           crc32+                           isize+       ) =+    "BAM_V1_6_BGZFBlock { "                               +++    "bam_v1_6_bgzfblock_gzip_header = "                   +++    (show gzip_header)                                    +++    " , bam_v1_6_bgzfblock_subfield_identifier_one = "    +++    (show subfield_identifier_one)                        +++    " , bam_v1_6_bgzfblock_subfield_identifier_two = "    +++    (show subfield_identifier_two)                        +++    " , bam_v1_6_bgzfblock_subfield_length = "            +++    (show subfield_length)                                +++    " , bam_v1_6_bgzfblock_total_block_size_minus_one = " +++    (show total_block_size_minus_one)                     +++    " , bam_v1_6_bgzfblock_cdata = "                      +++    (show cdata)                                          +++    " , bam_v1_6_bgzfblock_crc32 = "                      +++    (show crc32)                                          +++    " , bam_v1_6_bgzfblock_isize = "                      +++    (show isize)                                          +++    " }"

@@ -0,0 +1,51 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.Base+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.Base ( -- * BAM_V1_6 version 1.6 data type+                                  BAM_V1_6(..)+                                ) where++import Data.BAM.Version1_6.BGZFBlock++import Data.Data+import Data.Sequence+import Generics.Deriving.Base++-- | Custom @"BAM_V1_6"@ (BAM version 1.6) newtype.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+newtype BAM_V1_6 = BAM_V1_6+  { bam_v1_6 :: Seq BAM_V1_6_BGZFBlock -- ^ Sequence holding all+                                       -- BGZF blocks of data+                                       -- within the BAM file.+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6 where+  BAM_V1_6 bam_v1_61 ==+    BAM_V1_6 bam_v1_62 =+      bam_v1_61 == bam_v1_62++instance Show BAM_V1_6 where+  show (BAM_V1_6 bam+       ) =+    "BAM_V1_6 { " +++    "bam_v1_6 = " +++    (show bam)    +++    " }"

@@ -0,0 +1,98 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.GZipHeader+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.GZipHeader ( -- * BAM_V1_6_GZipHeader version 1.6 data type+                                        BAM_V1_6_GZipHeader(..)+                                      ) where++import Data.Data+import Data.Word+import Generics.Deriving.Base++-- | Custom @"BAM_V1_6_GZipHeader"@ (BAM version 1.6) data type.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_GZipHeader = BAM_V1_6_GZipHeader+  { bam_v1_6_gzip_header_gzip_identifier_1   :: Word8  -- ^ Magic number 1f (0x1f).+  , bam_v1_6_gzip_header_gzip_identifier_2   :: Word8  -- ^ Magic number 08 (0x08).+  , bam_v1_6_gzip_header_compression_method  :: Word8  -- ^ Compression method (08 for DEFLATE).+  , bam_v1_6_gzip_header_header_flags        :: Word8  -- ^ 1-byte for header flags.+  , bam_v1_6_gzip_header_modification_time   :: Word32 -- ^ 4-byte timestamp.+  , bam_v1_6_gzip_header_extra_flags         :: Word8  -- ^ 1-byte eXtra FLags.+  , bam_v1_6_gzip_header_operating_system    :: Word8  -- ^ The operating system id.+  , bam_v1_6_gzip_header_extra_length        :: Word16 -- ^ If FLG.FEXTRA is set,+                                                       -- this gives the length of the optional+                                                       -- extra field.+  } deriving (Generic,Typeable)++instance Eq BAM_V1_6_GZipHeader where+  BAM_V1_6_GZipHeader bam_v1_6_gzip_header_gzip_identifier_11+                      bam_v1_6_gzip_header_gzip_identifier_21+                      bam_v1_6_gzip_header_compression_method1+                      bam_v1_6_gzip_header_header_flags1+                      bam_v1_6_gzip_header_modification_time1+                      bam_v1_6_gzip_header_extra_flags1+                      bam_v1_6_gzip_header_operating_system_id1+                      bam_v1_6_gzip_header_extra_length1 ==+    BAM_V1_6_GZipHeader bam_v1_6_gzip_header_gzip_identifier_12+                        bam_v1_6_gzip_header_gzip_identifier_22+                        bam_v1_6_gzip_header_compression_method2+                        bam_v1_6_gzip_header_header_flags2+                        bam_v1_6_gzip_header_modification_time2+                        bam_v1_6_gzip_header_extra_flags2+                        bam_v1_6_gzip_header_operating_system_id2+                        bam_v1_6_gzip_header_extra_length2 =+      bam_v1_6_gzip_header_gzip_identifier_11   == bam_v1_6_gzip_header_gzip_identifier_12   &&+      bam_v1_6_gzip_header_gzip_identifier_21   == bam_v1_6_gzip_header_gzip_identifier_22   &&+      bam_v1_6_gzip_header_compression_method1  == bam_v1_6_gzip_header_compression_method2  &&+      bam_v1_6_gzip_header_header_flags1        == bam_v1_6_gzip_header_header_flags2        &&+      bam_v1_6_gzip_header_modification_time1   == bam_v1_6_gzip_header_modification_time2   &&+      bam_v1_6_gzip_header_extra_flags1         == bam_v1_6_gzip_header_extra_flags2         &&+      bam_v1_6_gzip_header_operating_system_id1 == bam_v1_6_gzip_header_operating_system_id2 &&+      bam_v1_6_gzip_header_extra_length1        == bam_v1_6_gzip_header_extra_length2++instance Show BAM_V1_6_GZipHeader where+  show (BAM_V1_6_GZipHeader gzip_identifier_1+                            gzip_identifier_2+                            compression_method+                            header_flags+                            modification_time+                            extra_flags+                            operating_system_id+                            extra_length+       ) =+    "BAM_V1_6_GZipHeader { "                         +++    "bam_v1_6_gzip_header_gzip_identifier_1 = "      +++    (show gzip_identifier_1)                         +++    " , bam_v1_6_gzip_header_gzip_identifier_2 = "   +++    (show gzip_identifier_2)                         +++    " , bam_v1_6_gzip_header_compression_method = "  +++    (show compression_method)                        +++    " , bam_v1_6_gzip_header_header_flags = "        +++    (show header_flags)                              +++    " , bam_v1_6_gzip_header_modification_time = "   +++    (show modification_time)                         +++    " , bam_v1_6_gzip_header_extra_flags = "         +++    (show extra_flags)                               +++    " , bam_v1_6_gzip_header_operating_system_id = " +++    (show operating_system_id)                       +++    " , bam_v1_6_gzip_header_extra_length = "        +++    (show extra_length)                              +++    " }"

@@ -0,0 +1,335 @@+{-# LANGUAGE FlexibleContexts #-}++-- |+-- Module      :  Data.BAM.Version1_6.Internal+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.Internal ( -- * BAM version 1.6 internal functions+                                      bytestringToFloatLE+                                    , byteStringToIntLE +                                    , byteStringToWord16LE+                                    , floatToByteStringLE+                                    , intToByteStringLE+                                    , intToWord16LE+                                    , intToWord32LE+                                    , int8ToByteString+                                    , int16ToByteStringLE+                                    , int32ToByteStringLE+                                    , maybeOption+                                    , splitByteString+                                    , word8sToInt8LE+                                    , word8sToInt16LE+                                    , word8sToInt32LE+                                    , word8sToWord8LE+                                    , word8sToWord16LE+                                    , word8sToWord32LE+                                    , word32ToByteStringLE+                                    , word16ToByteStringLE+                                    , word16ToByteString+                                    , word16ToIntLE+                                    ) where++import Data.Attoparsec.ByteString.Lazy+import Data.Binary.Get                 (runGet,getFloatle)+import Data.Binary.Put                 (runPut,putFloatle,putInt64le)+import Data.Bits+import Data.ByteString as DB+import Data.ByteString.Builder+import Data.Int+import Data.Word++-- | Make a parser optional, return Nothing if there is no match.+maybeOption :: Parser a+            -> Parser (Maybe a)+maybeOption p =+  option Nothing+         (Just <$> p)++-- | Convert a little-endian Word16 to an Int.+word16ToIntLE :: Word16+              -> Int+word16ToIntLE w = do+  let signedValue = fromIntegral w :: Int+      -- Check if the most significant bit (sign bit) is set+      isNegative = testBit signedValue 15+  case isNegative of+    True  ->+      signedValue - 65536  -- If negative, subtract 2^16+    False ->+      signedValue++-- | Split a ByteString into chunks of n bytes.+splitByteString :: Int+                -> ByteString+                -> [ByteString]+splitByteString n bs =+  case (DB.null bs) of+    True  ->+      []+    False ->+      case (DB.length bs `mod` n /= 0) of+        True  ->+          error $+            "ByteString length must be a multiple of " +++            (show n)                                   +++            "."+        False ->+          let (chunk,rest) = DB.splitAt n+                                        bs+            in chunk : splitByteString n+                                       rest++-- | Convert a ByteString to a Float (IEEE 754 binary32).+bytestringToFloatLE :: ByteString+                    -> Float+bytestringToFloatLE bs =+  case (DB.length bs == 4) of+    True  ->+      runGet getFloatle $+        fromStrict bs+    False ->+      error "ByteString must contain exactly 4 bytes"++-- | Convert a ByteString (little-endian) to an Int.+byteStringToIntLE :: ByteString+                  -> Int+byteStringToIntLE bs =+  Prelude.foldr go 0 (Prelude.zip [0..]+                                  (DB.unpack bs)+                     )+  where+    go :: (Int,Word8)+       -> Int+       -> Int+    go (i,b)+       acc = acc+             .|.+             ( fromIntegral b+               `shiftL`+               (8 * i)+             )++-- | Convert a ByteString to [Word16] in little-endian format.+byteStringToWord16LE :: ByteString+                     -> [Word16]+byteStringToWord16LE bs+  | DB.length bs `mod` 2 /= 0 = error "ByteString must have an even length."+  | otherwise = go bs+                   []+  where+    go :: ByteString+       -> [Word16]+       -> [Word16]+    go input acc+      | DB.null input = Prelude.reverse acc -- Stop processing when no bytes are left+      | otherwise     =+          let byte1  = fromIntegral (DB.index input 0) :: Word16 -- LSB+              byte2  = fromIntegral (DB.index input 1) :: Word16 -- MSB+              word16 = byte1 .|. (byte2 `shiftL` 8) -- Combine bytes in little-endian order+            in go ( DB.drop 2+                            input+                  )+                  ( word16 : acc+                  ) -- Recursively process the rest++-- | Convert a [Word8] to a Int8 (little endian).+word8sToInt8LE :: [Word8]+               -> Int8+word8sToInt8LE [ b0+               ] = fromIntegral b0+word8sToInt8LE _ = error "List must contain exactly 1 Word8 element."++-- | Convert a [Word8] to a Int16 (little endian).+word8sToInt16LE :: [Word8]+                -> Int16+word8sToInt16LE [ b0+                , b1+                ] = +  ( fromIntegral b0+  ) .|.+  ( fromIntegral b1+    `shiftL`+    8+  )+word8sToInt16LE _ = error "List must contain exactly 2 Word8 elements."++-- | Convert a [Word8] to a Int32 (little endian).+word8sToInt32LE :: [Word8]+              -> Int32+word8sToInt32LE [ b0+                , b1+                , b2+                , b3+                ] = +  (fromIntegral b0+  ) .|.+  ( fromIntegral b1+    `shiftL`+    8+  ) .|.+  ( fromIntegral b2+    `shiftL`+    16+  ) .|.+  ( fromIntegral b3+    `shiftL`+    24+  )+word8sToInt32LE _ = error "List must contain exactly 4 Word8 elements."++-- | Convert a [Word8] to a Word8 (little endian).+word8sToWord8LE :: [Word8]+                -> Word8+word8sToWord8LE [ b0+                ] = b0+word8sToWord8LE _ = error "List must contain exactly 1 Word8 element."++-- | Convert a [Word8] to a Word16 (little endian).+word8sToWord16LE :: [Word8]+                 -> Word16+word8sToWord16LE [ b0+                 , b1+                 ] = +  ( fromIntegral b0+  ) .|.+  ( fromIntegral b1+    `shiftL`+    8+  )+word8sToWord16LE _ = error "List must contain exactly 2 Word8 elements."++-- | Convert a [Word8] to a Word32 (little endian).+word8sToWord32LE :: [Word8]+                 -> Word32+word8sToWord32LE [ b0+                 , b1+                 , b2+                 , b3+                 ] =+  ( fromIntegral b0+  ) .|.+  ( fromIntegral b1+    `shiftL`+    8+  ) .|.+  ( fromIntegral b2+    `shiftL`+    16+  ) .|.+  ( fromIntegral b3+    `shiftL`+    24+  )+word8sToWord32LE _ = error "List must contain exactly 4 Word8 elements."++-- Convert Word16 to ByteString.+word16ToByteString :: Word16+                   -> ByteString+word16ToByteString w =+  DB.pack [ fromIntegral (w `shiftR` 8)+          , fromIntegral (w .&. 0xFF)+          ]++-- | Convert a Word16 in little endian+-- byte order to a ByteString.+word16ToByteStringLE :: Word16+                     -> ByteString+word16ToByteStringLE w =+  DB.toStrict        $+    toLazyByteString $+      word16LE w++-- | Convert a Word32 in little endian+-- byte order to a ByteString.+word32ToByteStringLE :: Word32+                     -> ByteString+word32ToByteStringLE w =+  DB.toStrict        $+    toLazyByteString $+      word32LE w++-- | Convert a Int in little endian+-- byte order to a ByteString.+intToByteStringLE :: Int+                  -> ByteString+intToByteStringLE i =+  DB.toStrict    $+    runPut       $+      putInt64le $+        fromIntegral i++-- | Convert an Int in little-endian+-- byte order to a Word16.+intToWord16LE :: Int+              -> Word16+intToWord16LE i+  | i >= 0 && i <= 0xFFFF = fromIntegral i+  | otherwise             = error "Int value is out of Word16 range"++-- | Convert an Int little-endian+-- byte order to a Word32.+intToWord32LE :: Int+              -> Word32+intToWord32LE i+  | i >= 0    = fromIntegral i+  | otherwise = error "Int value must be non-negative"++-- | Convert a Int8 in little endian+-- byte order to a ByteString.+int8ToByteString :: Int8+                 -> ByteString+int8ToByteString i =+  DB.toStrict        $+    toLazyByteString $+      int8 i++-- | Convert a Int16 in little endian+-- byte order to a ByteString.+int16ToByteStringLE :: Int16+                    -> ByteString+int16ToByteStringLE i =+  DB.toStrict        $+    toLazyByteString $+      int16LE i++-- | Convert a Int32 in little endian+-- byte order to a ByteString.+int32ToByteStringLE :: Int32+                    -> ByteString+int32ToByteStringLE i =+  DB.toStrict        $+    toLazyByteString $+      int32LE i++-- | Convert a Float in little endian+-- byte order to a ByteString.+-- See https://stackoverflow.com/questions/6976684/converting-ieee-754-floating-point-in-haskell-word32-64-to-and-from-haskell-floa+floatToByteStringLE :: Float+                    -> ByteString+floatToByteStringLE f =+  DB.toStrict $+    runPut    $+      putFloatle f

@@ -0,0 +1,113 @@+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.Read.Base+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.Read.Base ( -- * Reading+                                       readBAM_V1_6+                                     ) where++import Data.BAM.Version1_6.Base+import Data.BAM.Version1_6.Read.Error +import Data.BAM.Version1_6.Read.Parser.BGZFBlock++import           Data.Attoparsec.ByteString.Lazy   as DABL+import           Data.ByteString                   as DB+import           Data.ByteString.Lazy              as DBL+import           Data.Sequence                     as DSeq+import qualified Streamly.Data.Stream              as S+import           Streamly.External.ByteString.Lazy as StreamlyLByteString  (fromChunksIO)+import           Streamly.Internal.FileSystem.File as StreamlyInternalFile (chunkReader)+import qualified System.IO                         as SIO++-- | Define the @"BAM_V1_6"@ parser.+parse_BAM_V1_6 :: Parser BAM_V1_6+parse_BAM_V1_6 = do+  bgzfblocks <-+    DABL.many' parse_BAM_V1_6_BGZFBlock+  return BAM_V1_6+          { bam_v1_6 = DSeq.fromList bgzfblocks+          }++-- | Run the @"SAM_V1_6"@ parser.+readBAM_V1_6_LBS :: DBL.ByteString+                 -> IO BAM_V1_6+readBAM_V1_6_LBS lbs =+  case (DABL.parseOnly parse_BAM_V1_6 lbs) of +    Left  samparseerror ->+      error samparseerror+    Right sam           ->+      return sam++-- | Read a @"BAM_V1_6"@ from a file.+--+-- The file is checked for errors as it is parsed.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+readBAM_V1_6 :: FilePath -- ^ Input path to BAM file.+             -> IO BAM_V1_6+readBAM_V1_6 fp = do+  -- Ensure that BAM file is intact+  -- by checking for end-of-file+  -- marker.+  bamfileh        <-+    SIO.openBinaryFile fp+                       SIO.ReadMode+  _               <-+    SIO.hSeek bamfileh+              SIO.SeekFromEnd+              (-28)+  endoffilemarker <-+    DB.hGetContents bamfileh+  case ( endoffilemarker == endoffilemarkerbytes+       ) of+    False ->+      error $+        show BAM_V1_6_Read_Error_End_Of_File_Marker_Incorrect_Format+    True  -> do+      let lazybamfile = S.unfold StreamlyInternalFile.chunkReader fp+      lazybamfilef    <-+        StreamlyLByteString.fromChunksIO lazybamfile+      readBAM_V1_6_LBS lazybamfilef+  where+    endoffilemarkerbytes = DB.pack +                             [ 0x1f+                             , 0x8b+                             , 0x08+                             , 0x04+                             , 0x00+                             , 0x00+                             , 0x00+                             , 0x00+                             , 0x00+                             , 0xff+                             , 0x06+                             , 0x00+                             , 0x42+                             , 0x43+                             , 0x02+                             , 0x00+                             , 0x1b+                             , 0x00+                             , 0x03+                             , 0x00+                             , 0x00+                             , 0x00+                             , 0x00+                             , 0x00+                             , 0x00+                             , 0x00+                             , 0x00+                             , 0x00+                             ]

@@ -0,0 +1,319 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE StrictData            #-}+{-# LANGUAGE TypeFamilies          #-}++-- |+-- Module      :  Data.BAM.Version1_6.Read.Error+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.Read.Error ( -- * BAM version 1.6 data type+                                        BAM_V1_6_Read_Error(..)+                                      ) where++import Data.Data+import Generics.Deriving.Base++-- | Custom @"BAM_V1_6_Read_Error"@ (BAM version 1.6) error data type.+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data BAM_V1_6_Read_Error = -- | Identification 1 (IDentification 1; ID1) field+                           -- of the GZip header not in accepted format.+                           BAM_V1_6_Read_Error_GZipHeader_ID1_Incorrect_Format+                           -- | Identification 2 (IDentification 2; ID2) field+                           -- of the GZip header not in accepted format.+                         | BAM_V1_6_Read_Error_GZipHeader_ID2_Incorrect_Format+                           -- | Compression Method (CM) field of the GZip header not+                           -- in accepted format.+                         | BAM_V1_6_Read_Error_GZipHeader_Compression_Method_Incorrect_Format+                           -- | Flag (FLG) field of the GZip header not in accepted format.+                         | BAM_V1_6_Read_Error_GZipHeader_Flag_Incorrect_Format+                           -- | Modification TIME (MTIME) field of the GZip header not+                           -- in accepted format.+                         | BAM_V1_6_Read_Error_GZipHeader_Modification_TIME_Incorrect_Format+                           -- | Extra flags (eXtra FLags; XFL) field of the GZip header+                           -- not in accepted format.+                         | BAM_V1_6_Read_Error_GZipHeader_Extra_Flags_Incorrect_Format+                           -- | Operating System (OS) field of the GZip header+                           -- not in accepted format.+                         | BAM_V1_6_Read_Error_GZipHeader_Operating_System_Incorrect_Format+                           -- | Extra Length (eXtra LENgth; XLEN) field of the+                           -- GZip header is not in accepted format.+                         | BAM_V1_6_Read_Error_GZipHeader_Extra_Length_Incorrect_Format+                           -- | Subfield Identifier 1 (Subfield Identifier1; SI1)+                           -- field of the GZip header is not in accepted format.+                         | BAM_V1_6_Read_Error_GZipHeader_Subfield_Identifier_1_Incorrect_Format+                           -- | Subfield Identifier 2 (Subfield Identifier2; SI2)+                           -- field of the GZip header is not in accepted format.+                         | BAM_V1_6_Read_Error_GZipHeader_Subfield_Identifier_2_Incorrect_Format+                           -- | Subfield Length (Subfield LENgth; SLEN)+                           -- field of the GZip header is not in accepted format.+                         | BAM_V1_6_Read_Error_GZipHeader_Subfield_Length_Incorrect_Format+                           -- | Total block size minus 1 (total Block SIZE minus 1; BSIZE)+                           -- field of the GZip header is not in accepted format.+                         | BAM_V1_6_Read_Error_GZipHeader_Total_Block_SIZE_Minus_1_Incorrect_Format+                           -- | Compressed DATA by zlib::deflate() (CDATA) is not+                           -- in accepted format.+                         | BAM_V1_6_Read_Error_GZipHeader_Compressed_DATA_Incorrect_Format+                           -- | @HD tag not in accepted format (only important+                           -- if @HD tag is present).+                         | BAM_V1_6_Read_Error_File_Level_Metadata_Tag_Incorrect_Format+                           -- | VN tag missing (only important+                           -- if @HD tag is present).+                         | BAM_V1_6_Read_Error_File_Level_Metadata_Format_Version_Tag_Missing+                           -- | VN tag not in accepted format (only important+                           -- if @HD tag is present).+                         | BAM_V1_6_Read_Error_File_Level_Metadata_Format_Version_Tag_Incorrect_Format+                           -- | VN value not in accepted format (only important+                           -- if @HD tag is present).+                         | BAM_V1_6_Read_Error_File_Level_Metadata_Format_Version_Value_Incorrect_Format+                           -- | Sorting order tag not in accepted format (only important+                           -- if @HD tag is present).+                         | BAM_V1_6_Read_Error_File_Level_Metadata_Sorting_Order_Tag_Incorrect_Format+                           -- | Sorting order invalid value (only important+                           -- if @HD tag is present).+                         | BAM_V1_6_Read_Error_File_Level_Metadata_Sorting_Order_Invalid_Value+                           -- | Grouping of alignments no in accepted format (only important+                           -- if @HD tag is present).+                         | BAM_V1_6_Read_Error_File_Level_Metadata_Grouping_Of_Alignments_Tag_Incorrect_Format+                           -- | Grouping of Alignments invalid value (only important+                           -- if @HD tag is present).+                         | BAM_V1_6_Read_Error_File_Level_Metadata_Grouping_Of_Alignments_Invalid_Value+                           -- | Subsorting order tag not in accepted format (only important+                           -- if @HD tag is present).+                         | BAM_V1_6_Read_Error_File_Level_Metadata_Subsorting_Order_Tag_Incorrect_Format+                           -- | Subsorting order of alignments not in accepted format (only+                           -- if @HD tag is present.+                         | BAM_V1_6_Read_Error_File_Level_Metadata_Subsorting_Order_Incorrect_Format+                           -- | The BAM magic string in the BAM header is not BAM\SOH (BAM\1).+                         | BAM_V1_6_Read_Error_BAMHeader_BAM_Magic_String_Invalid_Value+                           -- | SN tag missing (only important+                           -- if @SQ tag is present).+                         | BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Reference_Sequence_Name_Tag_Missing+                           -- | Reference Sequence Name not in accepted format (only important+                           -- if @SQ tag is present.+                         | BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Reference_Sequence_Name_Incorrect_Format+                           -- | Reference Sequence Name invalid value (only important+                           -- if @SQ tag is present).+                         | BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Reference_Sequence_Name_Invalid_Value+                           -- | LN tag missing (only important+                           -- if @SQ tag is present).+                         |  BAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Length_Missing+                           -- | Reference Sequence Length not in accepted format (only important+                           -- if @SQ tag is present.+                         | BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Reference_Sequence_Length_Incorrect_Format+                           -- | Reference Sequence Length invalid value (only important+                           -- if @SQ tag is present).+                         | BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Reference_Sequence_Length_Invalid_Value+                           -- | Alternative locus not in accepted format (only important+                           -- if @SQ tag is present).+                         | BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Alternative_Locus_Incorrect_Format+                           -- | Alternative Reference Sequence Names not in accepted format (only important+                           -- if @SQ tag is present).+                         | BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names_Incorrect_Format+                           -- | Alternative Reference Sequence Names invalid value (only important+                           -- if @SQ tag is present).+                         | BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names_Invalid_Value+                           -- | Genome Assembly Identifier not in accepted format (only important+                           -- if @SQ tag is present).+                         | BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Genome_Assembly_Identifier_Incorrect_Format+                           -- | Description not in accepted format (only important+                           -- if @SQ tag is present).+                         | BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Description_Incorrect_Format+                           -- | MD5 checksum not in accepted format (only important+                           -- if @SQ tag is present).+                         | BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_MD5_Checksum_Incorrect_Format+                           -- | Species not in accepted format (only important+                           -- if @SQ tag is present).+                         | BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Species_Incorrect_Format+                           -- | Molecule topology not in accepted format (only important+                           -- if @SQ tag is present).+                         | BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Molecule_Topology_Incorrect_Format+                           -- | Molecule topology invalid value (only important+                           -- if @SQ tag is present).+                         | BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_Molecule_Topology_Invalid_Value+                           -- | URI not in accepted format (only important+                           -- if @SQ tag is present).+                         | BAM_V1_6_Read_Error_Reference_Sequence_Dictionary_URI_Incorrect_Format+                           -- | ID tag not accepted format (only important+                           -- if @RG tag is present).+                         | BAM_V1_6_Read_Error_Read_Group_Read_Group_Identifier_Incorrect_Format+                           -- | ID tag is missing (only important+                           -- if @RG tag is present).+                         | BAM_V1_6_Read_Error_Read_Group_Read_Group_Identifier_Tag_Missing+                           -- | BC tag not in accepted format (only important+                           -- if @RG tag is present).+                         | BAM_V1_6_Read_Error_Read_Group_Barcode_Sequence_Incorrect_Format+                           -- | CN tag not in accepted format (only important+                           -- if @RG tag is present).+                         | BAM_V1_6_Read_Error_Read_Group_Sequencing_Center_Incorrect_Format+                           -- | DS tag not in accepted format (only important+                           -- if @RG tag is present).+                         | BAM_V1_6_Read_Error_Read_Group_Description_Incorrect_Format+                           -- | DT tag not in accepted format (only important+                           -- if @RG tag is present).+                         | BAM_V1_6_Read_Error_Read_Group_Date_Run_Produced_Incorrect_Format+                           -- | FO tag not in accepted format (only important+                           -- if @RG tag is present).+                         | BAM_V1_6_Read_Error_Read_Group_Flow_Order_Incorrect_Format+                           -- | KS tag not in accepted format (only important+                           -- if @RG tag is present).+                         | BAM_V1_6_Read_Error_Read_Group_Key_Sequence_Incorrect_Format+                           -- | LB tag not in accepted format (only important+                           -- if @RG tag is present).+                         | BAM_V1_6_Read_Error_Read_Group_Library_Incorrect_Format+                           -- | PG tag not in accepted format (only important+                           -- if @RG tag is present).+                         | BAM_V1_6_Read_Error_Read_Group_Programs_Incorrect_Format+                           -- | PI tag not in accepted format (only important+                           -- if @RG tag is present).+                         | BAM_V1_6_Read_Error_Read_Group_Predicted_Median_Insert_Size_Incorrect_Format+                           -- | PL tag not in accepted format (only important+                           -- if @RG tag is present).+                         | BAM_V1_6_Read_Error_Read_Group_Platform_Incorrect_Format+                           -- | PM tag not in accepted format (only important+                           -- if @RG tag is present).+                         | BAM_V1_6_Read_Error_Read_Group_Platform_Model_Incorrect_Format+                           -- | PU tag not in accepted format (only important+                           -- if @RG tag is present).+                         | BAM_V1_6_Read_Error_Read_Group_Platform_Unit_Incorrect_Format+                           -- | SM tag not in accepted format (only important+                           -- if @RG tag is present).+                         | BAM_V1_6_Read_Error_Read_Group_Sample_Incorrect_Format+                           -- | RG tag not in accepted format.+                         | BAM_V1_6_Read_Error_Read_Group_Tag_Incorrect_Format+                           -- | ID tag not in accepted format (only important+                           -- if @PG tag is present).+                         | BAM_V1_6_Read_Error_Program_Identifier_Incorrect_Format+                           -- | PN tag not in accepted format (only important+                           -- if @PG tag is present).+                         | BAM_V1_6_Read_Error_Program_Name_Incorrect_Format+                           -- | CL tag not in accepted format (only important+                           -- if @PG tag is present).+                         | BAM_V1_6_Read_Error_Program_Command_Line_Incorrect_Format+                           -- | PP tag not in accepted format (only important+                           -- if @PG tag is present).+                         | BAM_V1_6_Read_Error_Program_Previous_PG_ID_Incorrect_Format+                           -- | DS tag not in accepted format (only important+                           -- if @PG tag is present).+                         | BAM_V1_6_Read_Error_Program_Description_Incorrect_Format+                           -- | VN tag not in accepted format (only important+                           -- if @PG tag is present).+                         | BAM_V1_6_Read_Error_Program_Version_Incorrect_Format+                           -- | PG tag not in accepted format.+                         | BAM_V1_6_Read_Error_Program_Tag_Incorrect_Format+                           -- | CO tag not in accepted format.+                         | BAM_V1_6_Read_Error_One_Line_Comment_Tag_Incorrect_Format+                           -- | QNAME of alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_QNAME_Incorrect_Format+                           -- | FLAG of alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_FLAG_Incorrect_Format+                           -- | RNAME of alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_RNAME_Incorrect_Format+                           -- | POS of alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_POS_Incorrect_Format+                           -- | MAPQ of alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_MAPQ_Incorrect_Format+                           -- | CIGAR of alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_CIGAR_Incorrect_Format+                           -- | RNEXT of alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_RNEXT_Incorrect_Format+                           -- | PNEXT of alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_PNEXT_Incorrect_Format+                           -- | TLEN of alignment section not in accpepted format.+                         | BAM_V1_6_Read_Error_Alignment_TLEN_Incorrect_Format+                           -- | SEQ of alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_SEQ_Incorrect_Format+                           -- | QUAL of alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_QUAL_Incorrect_Format+                           -- | Optional field is missing a type.+                         | BAM_V1_6_Read_Error_Alignment_OptionalFields_Missing_Type+                           -- | Optional field BOPT is missing a type.+                         | BAM_V1_6_Read_Error_Alignment_OptionalFields_BOPT_Missing_Type+                           -- | Optional field doesn't have a type.+                         | BAM_V1_6_Read_Error_Alignment_OptionalFields_Index_Missing+                           -- | Optional field has left-over bytes following parsing.+                         | BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes+                           -- | AOPT tag of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_AOPT_Tag_Incorrect_Format+                           -- | AOPT type of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_AOPT_Type_Incorrect_Format+                           -- | AOPT value of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_AOPT_Value_Incorrect_Format+                           -- | BigCOPT tag of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_BigCOPT_Tag_Incorrect_Format+                           -- | BigCOPT type of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_BigCOPT_Type_Incorrect_Format+                           -- | BigIOPT tag of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_BigIOPT_Tag_Incorrect_Format+                           -- | BigIOPT type of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_BigIOPT_Type_Incorrect_Format+                           -- | BigSOPT tag of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_BigSOPT_Tag_Incorrect_Format+                           -- | BigSOPT type of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_BigSOPT_Type_Incorrect_Format+                           -- | SmallCOPT tag of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_SmallCOPT_Tag_Incorrect_Format+                           -- | SmallCOPT type of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_SmallCOPT_Type_Incorrect_Format+                           -- | SmallIOPT tag of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_SmallIOPT_Tag_Incorrect_Format+                           -- | SmallIOPT type of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_SmallIOPT_Type_Incorrect_Format+                           -- | SmallSOPT tag of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_SmallSOPT_Tag_Incorrect_Format+                           -- | SmallSOPT type of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_SmallSOPT_Type_Incorrect_Format+                           -- | FOPT tag of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_FOPT_Tag_Incorrect_Format+                           -- | FOPT type of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_FOPT_Type_Incorrect_Format+                           -- | FOPT value of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_FOPT_Value_Incorrect_Format+                           -- | ZOPT tag of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_ZOPT_Tag_Incorrect_Format+                           -- | ZOPT type of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_ZOPT_Type_Incorrect_Format+                           -- | ZOPT value of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_ZOPT_Value_Incorrect_Format+                           -- | HOPT tag of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_HOPT_Tag_Incorrect_Format+                           -- | HOPT type of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_HOPT_Type_Incorrect_Format+                           -- | HOPT value of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_HOPT_Value_Incorrect_Format+                           -- | BOPT tag of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_BOPT_Tag_Incorrect_Format+                           -- | BOPT type of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_BOPT_Type_Incorrect_Format+                           -- | BOPT value type of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_BOPT_Value_Type_Incorrect_Format+                           -- | BOPT value data of the alignment section not in accepted format.+                         | BAM_V1_6_Read_Error_Alignment_BOPT_Value_Data_Incorrect_Format+                           -- | The CDATA field of a BGZF block not in accepted format.+                         | BAM_V1_6_Read_Error_CDATA_Incorrect_Format+                           -- | A CDATA BAM block alignment optional fields+                           -- are not in accepted format.+                         | BAM_V1_6_Read_Error_CDATA_BAM_Alignment_Optional_Fields_Incorrect_Format+                           -- | CRC-32 (CRC32) field of the GZip header+                           -- not in accepted format.+                         | BAM_V1_6_Read_Error_GZipHeader_CRC32_Incorrect_Format+                           -- | Input Size (Input SIZE, i.e. length of uncompressed data)+                           -- not in accepted format.+                         | BAM_V1_6_Read_Error_GZipHeader_Input_Size_Incorrect_Format+                           -- | The calculated crc32 of the uncompressed CDATA+                           -- is not equivalent to the CRC32 field of the BGZF block.+                         | BAM_V1_6_Read_Error_Calculated_CRC32_Not_Equivalent_To_CRC32+                           -- | The last 28 bytes of the BAM file are not equivalent+                           -- to the standardized 28 byte end-of-file marker.+                         | BAM_V1_6_Read_Error_End_Of_File_Marker_Incorrect_Format +  deriving (Eq,Generic,Show,Typeable)

@@ -0,0 +1,1117 @@+{-# LANGUAGE DeriveDataTypeable          #-}+{-# LANGUAGE DeriveGeneric               #-}+{-# LANGUAGE FlexibleContexts            #-}+{-# LANGUAGE FlexibleInstances           #-}+{-# LANGUAGE MultiParamTypeClasses       #-}+{-# LANGUAGE OverloadedLists             #-}+{-# LANGUAGE OverloadedStrings           #-}+{-# LANGUAGE MultiWayIf                  #-}+{-# LANGUAGE RecordWildCards             #-}+{-# LANGUAGE TypeFamilies                #-}+{-# LANGUAGE ViewPatterns                #-}+{-# Language QuasiQuotes                 #-}+{-# OPTIONS_GHC -fno-warn-name-shadowing #-}++-- |+-- Module      :  Data.BAM.Version1_6.Read.Parser.BAM.Alignment.Base+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.Read.Parser.BAM.Alignment.Base ( -- * BAM_V1_6_BAM parser - alignment section+                                                            parse_BAM_V1_6_BAM_Alignment+                                                          ) where++import Data.BAM.Version1_6.BAM.Alignment+import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.Base+import Data.BAM.Version1_6.Read.Error +import Data.BAM.Version1_6.Internal+import Data.BAM.Version1_6.Read.Parser.BAM.Alignment.Internal+import Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.AOPT+import Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BigCOPT+import Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BigIOPT+import Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BigSOPT+import Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.SmallCOPT+import Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.SmallIOPT+import Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.SmallSOPT+import Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.FOPT+import Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.ZOPT+import Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.HOPT+import Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BOPT++import Data.Attoparsec.ByteString.Lazy  as DABL+import Data.ByteString                  as DB hiding (intercalate,map)+import Data.List                                     (intercalate)+import Data.Sequence                    as DSeq      (empty,fromList,singleton,Seq(..))++-- | @"BAM_V1_6_BAM_Alignment"@ parser.+--+-- Defines a parser for the alignment section of the BAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_BAM_V1_6_BAM_Alignment :: Parser BAM_V1_6_BAM_Alignment+parse_BAM_V1_6_BAM_Alignment = do+  block_size  <-+    DABL.take 4+  refID       <-+    DABL.take 4+  pos         <-+    DABL.take 4+  l_read_name <-+    DABL.take 1+  mapq        <-+    DABL.take 1+  bin         <-+    DABL.take 2+  n_cigar_op  <-+    DABL.take 2+  flag        <-+    DABL.take 2+  l_seq       <-+    DABL.take 4+  next_refID  <-+    DABL.take 4 +  next_pos    <-+    DABL.take 4+  tlen        <-+    DABL.take 4+  read_name   <-+    DABL.take+      ( fromIntegral      $+          word8sToWord8LE $+            DB.unpack l_read_name :: Int+      )+  cigar       <-+    DABL.take+      ( ( ( fromIntegral       $+              word8sToWord16LE $+                DB.unpack n_cigar_op+          ) * 4+        ) :: Int+      )+  seq         <-+    DABL.take+      ( ( ( ( fromIntegral       $+                word8sToWord32LE $+                  DB.unpack l_seq+            ) + 1+          ) `div` 2+        ) :: Int+      )+  qual        <-+    DABL.take+      ( fromIntegral       $+          word8sToWord32LE $+            DB.unpack l_seq :: Int+      )+  let bytesuptooptionalfields = 4                                             + +                                4                                             ++                                1                                             ++                                1                                             + +                                2                                             ++                                2                                             ++                                2                                             ++                                4                                             ++                                4                                             ++                                4                                             ++                                4                                             ++                                ( fromIntegral      $+                                    word8sToWord8LE $+                                      DB.unpack l_read_name :: Int+                                )                                             ++                                ( ( ( fromIntegral       $+                                        word8sToWord16LE $+                                          DB.unpack n_cigar_op+                                    ) * 4+                                  ) :: Int+                                )                                             ++                                ( ( ( ( fromIntegral       $+                                          word8sToWord32LE $+                                            DB.unpack l_seq+                                      ) + 1+                                    ) `div` 2+                                  ) :: Int+                                )                                             ++                                ( fromIntegral       $+                                    word8sToWord32LE $+                                      DB.unpack l_seq+                                ) :: Int+  let block_size_int = fromIntegral       $+                         word8sToWord32LE $+                           DB.unpack block_size :: Int+  case (bytesuptooptionalfields == block_size_int) of+    True ->+      return BAM_V1_6_BAM_Alignment+               { bam_v1_6_bam_alignment_block_size     = word8sToWord32LE $+                                                           DB.unpack block_size+               , bam_v1_6_bam_alignment_refID          = word8sToInt32LE $+                                                           DB.unpack refID+               , bam_v1_6_bam_alignment_pos            = word8sToInt32LE $+                                                           DB.unpack pos+               , bam_v1_6_bam_alignment_l_read_name    = word8sToWord8LE $+                                                           DB.unpack l_read_name+               , bam_v1_6_bam_alignment_mapq           = word8sToWord8LE $+                                                           DB.unpack mapq+               , bam_v1_6_bam_alignment_bin            = word8sToWord16LE $+                                                           DB.unpack bin+               , bam_v1_6_bam_alignment_n_cigar_op     = word8sToWord16LE $+                                                           DB.unpack n_cigar_op+               , bam_v1_6_bam_alignment_flag           = word8sToWord16LE $+                                                           DB.unpack flag+               , bam_v1_6_bam_alignment_l_seq          = word8sToWord32LE $+                                                           DB.unpack l_seq+               , bam_v1_6_bam_alignment_next_refID     = word8sToInt32LE $+                                                           DB.unpack next_refID+               , bam_v1_6_bam_alignment_next_pos       = word8sToInt32LE $+                                                           DB.unpack next_pos+               , bam_v1_6_bam_alignment_tlen           = word8sToInt32LE $+                                                           DB.unpack tlen+               , bam_v1_6_bam_alignment_read_name      = read_name+               , bam_v1_6_bam_alignment_cigar          = DSeq.fromList                        $+                                                           map (word8sToWord32LE . DB.unpack) $+                                                             splitByteString 4+                                                                             cigar+               , bam_v1_6_bam_alignment_seq            = DSeq.fromList $+                                                           decodeSeqField seq+               , bam_v1_6_bam_alignment_qual           = qual+               , bam_v1_6_bam_alignment_optionalfields = DSeq.singleton+                                                           BAM_V1_6_BAM_Alignment_OptionalFields+                                                             { bam_v1_6_bam_alignment_optionalfields_aopt        = Nothing+                                                             , bam_v1_6_bam_alignment_optionalfields_smallcopt   = Nothing+                                                             , bam_v1_6_bam_alignment_optionalfields_bigcopt     = Nothing+                                                             , bam_v1_6_bam_alignment_optionalfields_smalliopt   = Nothing+                                                             , bam_v1_6_bam_alignment_optionalfields_bigiopt     = Nothing+                                                             , bam_v1_6_bam_alignment_optionalfields_smallsopt   = Nothing+                                                             , bam_v1_6_bam_alignment_optionalfields_bigsopt     = Nothing+                                                             , bam_v1_6_bam_alignment_optionalfields_fopt        = Nothing+                                                             , bam_v1_6_bam_alignment_optionalfields_zopt        = Nothing+                                                             , bam_v1_6_bam_alignment_optionalfields_hopt        = Nothing+                                                             , bam_v1_6_bam_alignment_optionalfields_bopt        = Nothing+                                                             }+               }+    False -> do+      -- This parser assumes that+      -- the optional alignment+      -- tags can appear in any order.+      optionalfieldbytes <-+        parse_BAM_V1_6_BAM_Alignment_OptionalFields block_size_int+                                                    bytesuptooptionalfields+      return BAM_V1_6_BAM_Alignment+               { bam_v1_6_bam_alignment_block_size     = word8sToWord32LE $+                                                           DB.unpack block_size+               , bam_v1_6_bam_alignment_refID          = word8sToInt32LE $+                                                           DB.unpack refID+               , bam_v1_6_bam_alignment_pos            = word8sToInt32LE $+                                                           DB.unpack pos+               , bam_v1_6_bam_alignment_l_read_name    = word8sToWord8LE $+                                                           DB.unpack l_read_name+               , bam_v1_6_bam_alignment_mapq           = word8sToWord8LE $+                                                           DB.unpack mapq+               , bam_v1_6_bam_alignment_bin            = word8sToWord16LE $+                                                           DB.unpack bin+               , bam_v1_6_bam_alignment_n_cigar_op     = word8sToWord16LE $+                                                           DB.unpack n_cigar_op+               , bam_v1_6_bam_alignment_flag           = word8sToWord16LE $+                                                           DB.unpack flag+               , bam_v1_6_bam_alignment_l_seq          = word8sToWord32LE $+                                                           DB.unpack l_seq+               , bam_v1_6_bam_alignment_next_refID     = word8sToInt32LE $+                                                           DB.unpack next_refID+               , bam_v1_6_bam_alignment_next_pos       = word8sToInt32LE $+                                                           DB.unpack next_pos+               , bam_v1_6_bam_alignment_tlen           = word8sToInt32LE $+                                                           DB.unpack tlen+               , bam_v1_6_bam_alignment_read_name      = read_name+               , bam_v1_6_bam_alignment_cigar          = DSeq.fromList                        $+                                                           map (word8sToWord32LE . DB.unpack) $+                                                             splitByteString 4+                                                                             cigar+               , bam_v1_6_bam_alignment_seq            = DSeq.fromList $+                                                           decodeSeqField seq+               , bam_v1_6_bam_alignment_qual           = qual+               , bam_v1_6_bam_alignment_optionalfields = optionalfieldbytes+               }+  where+    parse_BAM_V1_6_BAM_Alignment_OptionalFields :: Int+                                                -> Int+                                                -> Parser (Seq BAM_V1_6_BAM_Alignment_OptionalFields)+    parse_BAM_V1_6_BAM_Alignment_OptionalFields block_size_int+                                                bytesuptooptionalfields = do+      optionalfieldbytes' <-+        DABL.take $+          block_size_int -+          bytesuptooptionalfields+      return $+        parse_OptionalFields optionalfieldbytes'+      where+        parse_OptionalFields :: DB.ByteString+                             -> Seq BAM_V1_6_BAM_Alignment_OptionalFields +        parse_OptionalFields bs =+          case DB.null bs of+            True  ->+              DSeq.empty+            False ->+              case DB.indexMaybe bs 2 of+                Nothing                      ->+                  error $+                    show BAM_V1_6_Read_Error_Alignment_OptionalFields_Index_Missing+                -- AOPT <-> 'A'+                Just 0x41 ->+                  case ( DABL.parse parse_BAM_V1_6_BAM_Alignment_OptionalFields_AOPT+                                    ( DB.fromStrict $+                                        DB.take 4+                                                bs+                                    )+                       ) of+                    Fail _+                         ctxs+                         err ->+                      error  $+                        show $ "Error while parsing AOPT field." +++                               "\n"                              +++                               "Parsing contexts: "              +++                               (intercalate ", " ctxs)           +++                               "\n"                              +++                               "Error message: "                 +++                               err+                    Done remainingbytes+                         parsedbs -> do+                      let strictremainingbytes = DB.toStrict remainingbytes+                      case DB.null strictremainingbytes of+                        True  ->+                          BAM_V1_6_BAM_Alignment_OptionalFields+                            { bam_v1_6_bam_alignment_optionalfields_aopt        = Just parsedbs+                            , bam_v1_6_bam_alignment_optionalfields_smallcopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigcopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smalliopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigiopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smallsopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigsopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_fopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_zopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_hopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bopt        = Nothing+                            }+                          DSeq.:<|+                          parse_OptionalFields ( DB.drop 4+                                                         bs+                                               )+                        False ->+                          error $+                            show BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes+                -- SmallCOPT <-> 'c'+                Just 0x63 ->+                  case ( DABL.parse parse_BAM_V1_6_BAM_Alignment_OptionalFields_SmallCOPT+                                    ( DB.fromStrict $+                                        DB.take 4+                                                bs+                                    )+                       ) of+                    Fail _+                         ctxs+                         err ->+                      error  $+                        show $ "Error while parsing SmallCOPT field." +++                               "\n"                                   +++                               "Parsing contexts: "                   +++                               (intercalate ", " ctxs)                +++                               "\n"                                   +++                               "Error message: "                      +++                               err+                    Done remainingbytes+                         parsedbs -> do+                      let strictremainingbytes = DB.toStrict remainingbytes+                      case DB.null strictremainingbytes of+                        True  ->+                          BAM_V1_6_BAM_Alignment_OptionalFields+                            { bam_v1_6_bam_alignment_optionalfields_aopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smallcopt   = Just parsedbs+                            , bam_v1_6_bam_alignment_optionalfields_bigcopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smalliopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigiopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smallsopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigsopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_fopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_zopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_hopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bopt        = Nothing+                            }+                          DSeq.:<|+                          parse_OptionalFields ( DB.drop 4+                                                         bs+                                               )+                        False ->+                          error $+                            show BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes+                -- BigCOPT <-> 'C'+                Just 0x43 ->+                  case ( DABL.parse parse_BAM_V1_6_BAM_Alignment_OptionalFields_BigCOPT+                                    ( DB.fromStrict $+                                        DB.take 4+                                                bs+                                    )+                       ) of+                    Fail _+                         ctxs+                         err ->+                      error  $+                        show $ "Error while parsing BigCOPT field." +++                               "\n"                                 +++                               "Parsing contexts: "                 +++                               (intercalate ", " ctxs)              +++                               "\n"                                 +++                               "Error message: "                    +++                               err+                    Done remainingbytes+                         parsedbs -> do+                      let strictremainingbytes = DB.toStrict remainingbytes+                      case DB.null strictremainingbytes of+                        True  ->+                          BAM_V1_6_BAM_Alignment_OptionalFields+                            { bam_v1_6_bam_alignment_optionalfields_aopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smallcopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigcopt     = Just parsedbs+                            , bam_v1_6_bam_alignment_optionalfields_smalliopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigiopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smallsopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigsopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_fopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_zopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_hopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bopt        = Nothing+                            }+                          DSeq.:<|+                          parse_OptionalFields ( DB.drop 4+                                                         bs+                                               )+                        False ->+                          error $+                            show BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes+                -- SmallIOPT <-> 'i'+                Just 0x69 ->+                  case ( DABL.parse parse_BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT+                                    ( DB.fromStrict $+                                        DB.take 7+                                                bs+                                    )+                       ) of+                    Fail _+                         ctxs+                         err ->+                      error  $+                        show $ "Error while parsing SmallIOPT field." +++                               "\n"                                   +++                               "Parsing contexts: "                   +++                               (intercalate ", " ctxs)                +++                               "\n"                                   +++                               "Error message: "                      +++                               err+                    Done remainingbytes+                         parsedbs -> do+                      let strictremainingbytes = DB.toStrict remainingbytes+                      case DB.null strictremainingbytes of+                        True  ->+                          BAM_V1_6_BAM_Alignment_OptionalFields+                            { bam_v1_6_bam_alignment_optionalfields_aopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smallcopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigcopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smalliopt   = Just parsedbs+                            , bam_v1_6_bam_alignment_optionalfields_bigiopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smallsopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigsopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_fopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_zopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_hopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bopt        = Nothing+                            }+                          DSeq.:<|+                          parse_OptionalFields ( DB.drop 7+                                                         bs+                                               ) +                        False ->+                          error $+                            show BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes+                -- BigIOPT <-> 'I'+                Just 0x49 ->+                  case ( DABL.parse parse_BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT+                                    ( DB.fromStrict $+                                        DB.take 7+                                                bs+                                    )+                       ) of+                    Fail _+                         ctxs+                         err ->+                      error  $+                        show $ "Error while parsing BigIOPT field." +++                               "\n"                                 +++                               "Parsing contexts: "                 +++                               (intercalate ", " ctxs)              +++                               "\n"                                 +++                               "Error message: "                    +++                               err+                    Done remainingbytes+                         parsedbs -> do+                      let strictremainingbytes = DB.toStrict remainingbytes+                      case DB.null strictremainingbytes of+                        True  ->+                          BAM_V1_6_BAM_Alignment_OptionalFields+                            { bam_v1_6_bam_alignment_optionalfields_aopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smallcopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigcopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smalliopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigiopt     = Just parsedbs+                            , bam_v1_6_bam_alignment_optionalfields_smallsopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigsopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_fopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_zopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_hopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bopt        = Nothing+                            }+                          DSeq.:<|+                          parse_OptionalFields ( DB.drop 7+                                                         bs+                                               )+                        False ->+                          error $+                            show BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes+                -- SmallSOPT <-> 's'+                Just 0x73 ->+                  case ( DABL.parse parse_BAM_V1_6_BAM_Alignment_OptionalFields_SmallSOPT+                                    ( DB.fromStrict $+                                        DB.take 5+                                                bs+                                    )+                       ) of+                    Fail _+                         ctxs+                         err ->+                      error  $+                        show $ "Error while parsing SmallSOPT field." +++                               "\n"                                   +++                               "Parsing contexts: "                   +++                               (intercalate ", " ctxs)                +++                               "\n"                                   +++                               "Error message: "                      +++                               err+                    Done remainingbytes+                         parsedbs -> do+                      let strictremainingbytes = DB.toStrict remainingbytes+                      case DB.null strictremainingbytes of+                        True  ->+                          BAM_V1_6_BAM_Alignment_OptionalFields+                            { bam_v1_6_bam_alignment_optionalfields_aopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smallcopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigcopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smalliopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigiopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smallsopt   = Just parsedbs+                            , bam_v1_6_bam_alignment_optionalfields_bigsopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_fopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_zopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_hopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bopt        = Nothing+                            }+                          DSeq.:<|+                          parse_OptionalFields ( DB.drop 5+                                                         bs+                                               )+                        False ->+                          error $+                            show BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes+                -- BigSOPT <-> 'S'+                Just 0x53 ->+                  case ( DABL.parse parse_BAM_V1_6_BAM_Alignment_OptionalFields_BigSOPT+                                    ( DB.fromStrict $+                                        DB.take 5+                                                bs+                                    )+                       ) of+                    Fail _+                         ctxs+                         err ->+                      error  $+                        show $ "Error while parsing BigSOPT field." +++                               "\n"                                 +++                               "Parsing contexts: "                 +++                               (intercalate ", " ctxs)              +++                               "\n"                                 +++                               "Error message: "                    +++                               err+                    Done remainingbytes+                         parsedbs -> do+                      let strictremainingbytes = DB.toStrict remainingbytes+                      case DB.null strictremainingbytes of+                        True  ->+                          BAM_V1_6_BAM_Alignment_OptionalFields+                            { bam_v1_6_bam_alignment_optionalfields_aopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smallcopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigcopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smalliopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigiopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smallsopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigsopt     = Just parsedbs+                            , bam_v1_6_bam_alignment_optionalfields_fopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_zopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_hopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bopt        = Nothing+                            }+                          DSeq.:<|+                          parse_OptionalFields ( DB.drop 5+                                                         bs+                                               )+                        False ->+                          error $+                            show BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes+                -- FOPT <-> 'f'+                Just 0x66 ->+                  case ( DABL.parse parse_BAM_V1_6_BAM_Alignment_OptionalFields_FOPT+                                    ( DB.fromStrict $+                                        DB.take 7+                                                bs+                                    )+                       ) of+                    Fail _+                         ctxs+                         err ->+                      error  $+                        show $ "Error while parsing FOPT field." +++                               "\n"                              +++                               "Parsing contexts: "              +++                               (intercalate ", " ctxs)           +++                               "\n"                              +++                               "Error message: "                 +++                               err+                    Done remainingbytes+                         parsedbs -> do+                      let strictremainingbytes = DB.toStrict remainingbytes+                      case DB.null strictremainingbytes of+                        True  ->+                          BAM_V1_6_BAM_Alignment_OptionalFields+                            { bam_v1_6_bam_alignment_optionalfields_aopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smallcopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigcopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smalliopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigiopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smallsopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigsopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_fopt        = Just parsedbs+                            , bam_v1_6_bam_alignment_optionalfields_zopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_hopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bopt        = Nothing+                            }+                          DSeq.:<|+                          parse_OptionalFields ( DB.drop 7+                                                         bs+                                               )+                        False ->+                          error $+                            show BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes+                -- ZOPT <-> 'Z'+                Just 0x5A ->+                  case ( DABL.parse parse_BAM_V1_6_BAM_Alignment_OptionalFields_ZOPT+                                    ( DB.fromStrict $+                                        takeUpTo 0x00+                                                 bs+                                    )+                       ) of+                    Fail _+                         ctxs+                         err ->+                      error  $+                        show $ "Error while parsing ZOPT field." +++                               "\n"                              +++                               "Parsing contexts: "              +++                               (intercalate ", " ctxs)           +++                               "\n"                              +++                               "Error message: "                 +++                               err+                    Done remainingbytes+                         parsedbs -> do+                      let strictremainingbytes = DB.toStrict remainingbytes+                      case DB.null strictremainingbytes of+                        True  ->+                          BAM_V1_6_BAM_Alignment_OptionalFields+                            { bam_v1_6_bam_alignment_optionalfields_aopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smallcopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigcopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smalliopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigiopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smallsopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigsopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_fopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_zopt        = Just parsedbs+                            , bam_v1_6_bam_alignment_optionalfields_hopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bopt        = Nothing+                            }+                          DSeq.:<|+                          parse_OptionalFields ( dropUpTo 0x00+                                                          bs+                                               )+                        False ->+                          error $+                            show BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes+                -- HOPT <-> 'H'+                Just 0x48 ->+                  case ( DABL.parse parse_BAM_V1_6_BAM_Alignment_OptionalFields_HOPT+                                    ( DB.fromStrict $+                                        takeUpTo 0x00+                                                 bs+                                    )+                       ) of+                    Fail _+                         ctxs+                         err ->+                      error  $+                        show $ "Error while parsing HOPT field." +++                               "\n"                              +++                               "Parsing contexts: "              +++                               (intercalate ", " ctxs)           +++                               "\n"                              +++                               "Error message: "                 +++                               err+                    Done remainingbytes+                         parsedbs -> do+                      let strictremainingbytes = DB.toStrict remainingbytes+                      case DB.null strictremainingbytes of+                        True  ->+                          BAM_V1_6_BAM_Alignment_OptionalFields+                            { bam_v1_6_bam_alignment_optionalfields_aopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smallcopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigcopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smalliopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigiopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_smallsopt   = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_bigsopt     = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_fopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_zopt        = Nothing+                            , bam_v1_6_bam_alignment_optionalfields_hopt        = Just parsedbs+                            , bam_v1_6_bam_alignment_optionalfields_bopt        = Nothing+                            }+                          DSeq.:<|+                          parse_OptionalFields ( dropUpTo 0x00+                                                          bs+                                               )+                        False ->+                          error $+                            show BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes+                -- BOPT <-> 'B'+                Just 0x42 ->+                  case DB.indexMaybe bs 3 of+                    Nothing            ->+                      error $+                        show BAM_V1_6_Read_Error_Alignment_OptionalFields_Missing_Type+                    Just boptcharacter ->+                      case boptcharacter of+                        -- 'c'+                        0x63 -> do+                          let boptcount = fromIntegral       $+                                            word8sToWord32LE $+                                              DB.unpack      $+                                                DB.take 4    $+                                                  DB.drop 4+                                                          bs+                          case ( DABL.parse parse_BAM_V1_6_BAM_Alignment_OptionalFields_BOPT+                                            ( DB.fromStrict $+                                                DB.take+                                                  ( ( boptcount * 1+                                                    ) + 8+                                                  )+                                                  bs+                                            )+                               ) of+                            Fail _+                                 ctxs+                                 err ->+                              error  $+                                show $ "Error while parsing BOPT field." +++                                       "\n"                              +++                                       "Parsing contexts: "              +++                                       (intercalate ", " ctxs)           +++                                       "\n"                              +++                                       "Error message: "                 +++                                       err+                            Done remainingbytes+                                 parsedbs -> do+                              let strictremainingbytes = DB.toStrict remainingbytes+                              case DB.null strictremainingbytes of+                                True  ->+                                  BAM_V1_6_BAM_Alignment_OptionalFields+                                    { bam_v1_6_bam_alignment_optionalfields_aopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smallcopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigcopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smalliopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigiopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smallsopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigsopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_fopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_zopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_hopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bopt        = Just parsedbs+                                    }+                                  DSeq.:<|+                                  parse_OptionalFields ( DB.drop ( ( boptcount * 1+                                                                   ) + 8+                                                                 )+                                                                 bs+                                                       )+                                False ->+                                  error $+                                    show BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes+                        -- 'C'+                        0x43 -> do+                          let boptcount = fromIntegral       $+                                            word8sToWord32LE $+                                              DB.unpack      $+                                                DB.take 4    $+                                                  DB.drop 4+                                                          bs+                          case ( DABL.parse parse_BAM_V1_6_BAM_Alignment_OptionalFields_BOPT+                                            ( DB.fromStrict $+                                                DB.take+                                                  ( ( boptcount * 1+                                                    ) + 8+                                                  )+                                                  bs+                                            )+                               ) of+                            Fail _+                                 ctxs+                                 err ->+                              error  $+                                show $ "Error while parsing BOPT field." +++                                       "\n"                              +++                                       "Parsing contexts: "              +++                                       (intercalate ", " ctxs)           +++                                       "\n"                              +++                                       "Error message: "                 +++                                       err+                            Done remainingbytes+                                 parsedbs -> do+                              let strictremainingbytes = DB.toStrict remainingbytes+                              case DB.null strictremainingbytes of+                                True  ->+                                  BAM_V1_6_BAM_Alignment_OptionalFields+                                    { bam_v1_6_bam_alignment_optionalfields_aopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smallcopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigcopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smalliopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigiopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smallsopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigsopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_fopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_zopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_hopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bopt        = Just parsedbs+                                    }+                                  DSeq.:<|+                                  parse_OptionalFields ( DB.drop ( ( boptcount * 1+                                                                   ) + 8+                                                                 )+                                                                 bs+                                                       )+                                False ->+                                  error $+                                    show BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes+                        -- 'i'+                        0x69 -> do+                          let boptcount = fromIntegral       $+                                            word8sToWord32LE $+                                              DB.unpack      $+                                                DB.take 4    $+                                                  DB.drop 4+                                                          bs+                          case ( DABL.parse parse_BAM_V1_6_BAM_Alignment_OptionalFields_BOPT+                                            ( DB.fromStrict $+                                                DB.take+                                                  ( ( boptcount * 4+                                                    ) + 8+                                                  )+                                                  bs+                                            )+                               ) of+                            Fail _+                                 ctxs+                                 err ->+                              error  $+                                show $ "Error while parsing BOPT field." +++                                       "\n"                              +++                                       "Parsing contexts: "              +++                                       (intercalate ", " ctxs)           +++                                       "\n"                              +++                                       "Error message: "                 +++                                       err+                            Done remainingbytes+                                 parsedbs -> do+                              let strictremainingbytes = DB.toStrict remainingbytes+                              case DB.null strictremainingbytes of+                                True  ->+                                  BAM_V1_6_BAM_Alignment_OptionalFields+                                    { bam_v1_6_bam_alignment_optionalfields_aopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smallcopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigcopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smalliopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigiopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smallsopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigsopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_fopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_zopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_hopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bopt        = Just parsedbs+                                    }+                                  DSeq.:<|+                                  parse_OptionalFields ( DB.drop ( ( boptcount * 4+                                                                   ) + 8+                                                                 )+                                                                 bs+                                                       )+                                False ->+                                  error $+                                    show BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes+                        -- 'I'+                        0x49 -> do+                          let boptcount = fromIntegral       $+                                            word8sToWord32LE $+                                              DB.unpack      $+                                                DB.take 4    $+                                                  DB.drop 4+                                                          bs+                          case ( DABL.parse parse_BAM_V1_6_BAM_Alignment_OptionalFields_BOPT+                                            ( DB.fromStrict $+                                                DB.take+                                                  ( ( boptcount * 4+                                                    ) + 8+                                                  )+                                                  bs+                                            )+                               ) of+                            Fail _+                                 ctxs+                                 err ->+                              error  $+                                show $ "Error while parsing BOPT field." +++                                       "\n"                              +++                                       "Parsing contexts: "              +++                                       (intercalate ", " ctxs)           +++                                       "\n"                              +++                                       "Error message: "                 +++                                       err+                            Done remainingbytes+                                 parsedbs -> do+                              let strictremainingbytes = DB.toStrict remainingbytes+                              case DB.null strictremainingbytes of+                                True  ->+                                  BAM_V1_6_BAM_Alignment_OptionalFields+                                    { bam_v1_6_bam_alignment_optionalfields_aopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smallcopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigcopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smalliopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigiopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smallsopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigsopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_fopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_zopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_hopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bopt        = Just parsedbs+                                    }+                                  DSeq.:<|+                                  parse_OptionalFields ( DB.drop ( ( boptcount * 4+                                                                   ) + 8+                                                                 )+                                                                 bs+                                                       )+                                False ->+                                  error $+                                    show BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes+                        -- 's'+                        0x73 -> do+                          let boptcount = fromIntegral       $+                                            word8sToWord32LE $+                                              DB.unpack      $+                                                DB.take 4    $+                                                  DB.drop 4+                                                          bs+                          case ( DABL.parse parse_BAM_V1_6_BAM_Alignment_OptionalFields_BOPT+                                            ( DB.fromStrict $+                                                DB.take+                                                  ( ( boptcount * 2+                                                    ) + 8+                                                  )+                                                  bs+                                            )+                               ) of+                            Fail _+                                 ctxs+                                 err ->+                              error  $+                                show $ "Error while parsing BOPT field." +++                                       "\n"                              +++                                       "Parsing contexts: "              +++                                       (intercalate ", " ctxs)           +++                                       "\n"                              +++                                       "Error message: "                 +++                                       err+                            Done remainingbytes+                                 parsedbs -> do+                              let strictremainingbytes = DB.toStrict remainingbytes+                              case DB.null strictremainingbytes of+                                True  ->+                                  BAM_V1_6_BAM_Alignment_OptionalFields+                                    { bam_v1_6_bam_alignment_optionalfields_aopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smallcopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigcopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smalliopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigiopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smallsopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigsopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_fopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_zopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_hopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bopt        = Just parsedbs+                                    }+                                  DSeq.:<|+                                  parse_OptionalFields ( DB.drop ( ( boptcount * 2+                                                                   ) + 8+                                                                 )+                                                                 bs+                                                       )+                                False ->+                                  error $+                                    show BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes+                        -- 'S'+                        0x53 -> do+                          let boptcount = fromIntegral       $+                                            word8sToWord32LE $+                                              DB.unpack      $+                                                DB.take 4    $+                                                  DB.drop 4+                                                          bs+                          case ( DABL.parse parse_BAM_V1_6_BAM_Alignment_OptionalFields_BOPT+                                            ( DB.fromStrict $+                                                DB.take+                                                  ( ( boptcount * 2+                                                    ) + 8+                                                  )+                                                  bs+                                            )+                               ) of+                            Fail _+                                 ctxs+                                 err ->+                              error  $+                                show $ "Error while parsing BOPT field." +++                                       "\n"                              +++                                       "Parsing contexts: "              +++                                       (intercalate ", " ctxs)           +++                                       "\n"                              +++                                       "Error message: "                 +++                                       err+                            Done remainingbytes+                                 parsedbs -> do+                              let strictremainingbytes = DB.toStrict remainingbytes+                              case DB.null strictremainingbytes of+                                True  ->+                                  BAM_V1_6_BAM_Alignment_OptionalFields+                                    { bam_v1_6_bam_alignment_optionalfields_aopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smallcopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigcopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smalliopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigiopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smallsopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigsopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_fopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_zopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_hopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bopt        = Just parsedbs+                                    }+                                  DSeq.:<|+                                  parse_OptionalFields ( DB.drop ( ( boptcount * 2+                                                                   ) + 8+                                                                 )+                                                                 bs+                                                       )+                                False ->+                                  error $+                                    show BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes+                        -- 'f'+                        0x66 -> do+                          let boptcount = fromIntegral       $+                                            word8sToWord32LE $+                                              DB.unpack      $+                                                DB.take 4    $+                                                  DB.drop 4+                                                          bs+                          case ( DABL.parse parse_BAM_V1_6_BAM_Alignment_OptionalFields_BOPT+                                            ( DB.fromStrict $+                                                DB.take+                                                  ( ( boptcount * 4+                                                    ) + 8+                                                  )+                                                  bs+                                            )+                               ) of+                            Fail _+                                 ctxs+                                 err ->+                              error  $+                                show $ "Error while parsing BOPT field." +++                                       "\n"                              +++                                       "Parsing contexts: "              +++                                       (intercalate ", " ctxs)           +++                                       "\n"                              +++                                       "Error message: "                 +++                                       err+                            Done remainingbytes+                                 parsedbs -> do+                              let strictremainingbytes = DB.toStrict remainingbytes+                              case DB.null strictremainingbytes of+                                True  ->+                                  BAM_V1_6_BAM_Alignment_OptionalFields+                                    { bam_v1_6_bam_alignment_optionalfields_aopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smallcopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigcopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smalliopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigiopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_smallsopt   = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bigsopt     = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_fopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_zopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_hopt        = Nothing+                                    , bam_v1_6_bam_alignment_optionalfields_bopt        = Just parsedbs+                                    }+                                  DSeq.:<|+                                  parse_OptionalFields ( DB.drop ( ( boptcount * 4+                                                                   ) + 8+                                                                 )+                                                                 bs+                                                       )+                                False ->+                                  error $+                                    show BAM_V1_6_Read_Error_Alignment_OptionalFields_Remaining_Bytes+                        _    ->+                          error $+                            show BAM_V1_6_Read_Error_Alignment_OptionalFields_BOPT_Missing_Type+                _         ->+                  error $+                    show BAM_V1_6_Read_Error_Alignment_OptionalFields_Missing_Type

@@ -0,0 +1,79 @@+-- |+-- Module      :  Data.BAM.Version1_6.Read.Parser.BAM.Alignment.Internal+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.Read.Parser.BAM.Alignment.Internal ( -- * BAM_V1_6_BAM_BAMAlignments parser - internal functions+                                                                decodeSeqField  +                                                              , dropUpTo+                                                              , takeUpTo+                                                              ) where++import Data.Bits+import Data.ByteString as DB hiding (concatMap)+import Data.Word++-- | Decode SEQ field to a [Word8]+-- (each byte represents two bases).+decodeSeqField :: DB.ByteString+               -> [Word8]+decodeSeqField bytes =+  concatMap decodeByte (DB.unpack bytes)+  where+    decodeByte :: Word8+               -> [Word8]+    decodeByte byte =+      [ byte `shiftR` 4+      , byte .&. 0x0F+      ]++-- | Extract a sub ByteString starting from+-- and including the first occurrence of the given byte.+dropUpTo :: Word8+         -> ByteString+         -> ByteString+dropUpTo byte bs = +  let (_,suffix) = DB.break (== byte) bs+    in case DB.uncons suffix of+         Nothing ->+           DB.empty -- Specified byte not found, return an empty ByteString.+         Just _  ->+           suffix++-- | Extract a sub ByteString up to+-- and including the first occurrence of a given byte.+takeUpTo :: Word8+         -> ByteString+         -> ByteString+takeUpTo byte+         bs = +  let (prefix,suffix) = DB.break (== byte) bs+    in case DB.uncons suffix of+         Nothing    ->+           prefix -- No 0x00 found, return the entire ByteString.+         Just (_,_) ->+           DB.concat [ prefix+                     , DB.singleton byte+                     ]

@@ -0,0 +1,92 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.AOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.AOPT ( -- * BAM_V1_6_BAM parser - alignment section - aopt field +                                                                           parse_BAM_V1_6_BAM_Alignment_OptionalFields_AOPT+                                                                         ) where++import           Data.BAM.Version1_6.BAM.Alignment.OptionalFields.AOPT+import           Data.BAM.Version1_6.Internal+import           Data.BAM.Version1_6.Read.Error++import           Data.ByteString                 as DB+import           Data.Attoparsec.ByteString.Lazy as DABL+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the optional aopt field of alignment section of the BAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_BAM_V1_6_BAM_Alignment_OptionalFields_AOPT :: Parser BAM_V1_6_BAM_Alignment_OptionalFields_AOPT+parse_BAM_V1_6_BAM_Alignment_OptionalFields_AOPT = do+  alignmentaoptfieldtag <- do+    alignmentaoptfieldtagp <-+      DABL.take 2+    -- Parse AOPT tag of the alignment section.+    case (alignmentaoptfieldtagp =~ [re|[A-Za-z][A-Za-z0-9]|]) of+      False ->+        fail $ show BAM_V1_6_Read_Error_Alignment_AOPT_Tag_Incorrect_Format+      True  ->+        -- AOPT tag is in the accepted format. +        return alignmentaoptfieldtagp+  _ <- do+    alignmentaoptfieldtypep <-+      DABL.take 1+    -- Parse AOPT type of the alignment section.+    case (alignmentaoptfieldtypep =~ [re|[A]|]) of+      False ->+        fail $ show BAM_V1_6_Read_Error_Alignment_AOPT_Type_Incorrect_Format+      True  ->+        -- AOPT type is in the accepted format.+        return ()+  alignmentaoptfieldvalue <- do+    alignmentaoptfieldvaluep <-+      DABL.take 1 +    -- Parse AOPT value of the alignment section.+    case (alignmentaoptfieldvaluep =~ [re|[!-~]|]) of+      False ->+        fail $ show BAM_V1_6_Read_Error_Alignment_AOPT_Value_Incorrect_Format+      True  ->+        -- AOPT value is in the accepted format.+        return alignmentaoptfieldvaluep+  return BAM_V1_6_BAM_Alignment_OptionalFields_AOPT+           { bam_v1_6_bam_alignment_optionalfields_aopt_tag   = alignmentaoptfieldtag+           , bam_v1_6_bam_alignment_optionalfields_aopt_value = word8sToWord8LE $+                                                                  DB.unpack alignmentaoptfieldvalue+           }

@@ -0,0 +1,343 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BOPT ( -- * BAM_V1_6_BAM parser - alignment section - bopt field +                                                                           parse_BAM_V1_6_BAM_Alignment_OptionalFields_BOPT+                                                                         ) where++import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BOPT+import Data.BAM.Version1_6.Internal+import Data.BAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy as DABL+import qualified Data.ByteString                 as DB (unpack)+import qualified Data.ByteString.Char8           as DBC8+import           Data.Sequence                   as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the optional bopt field of alignment section of the BAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_BAM_V1_6_BAM_Alignment_OptionalFields_BOPT :: Parser BAM_V1_6_BAM_Alignment_OptionalFields_BOPT+parse_BAM_V1_6_BAM_Alignment_OptionalFields_BOPT = do+  alignmentboptfieldtag <- do+    alignmentboptfieldtagp <-+      DABL.take 2+    -- Parse BOPT tag of the alignment section.+    case (alignmentboptfieldtagp =~ [re|[A-Za-z][A-Za-z0-9]|]) of+      False ->+        fail $+          show BAM_V1_6_Read_Error_Alignment_BOPT_Tag_Incorrect_Format+      True  ->+        -- BOPT tag is in the accepted format. +        return alignmentboptfieldtagp+  _ <- do+    alignmentboptfieldtypep <-+      DABL.take 1+    -- Parse BOPT type of the alignment section.+    case (alignmentboptfieldtypep =~ [re|[B]|]) of+      False ->+        fail $+          show BAM_V1_6_Read_Error_Alignment_BOPT_Type_Incorrect_Format+      True  ->+        -- BOPT type is in the accepted format.+        return ()+  alignmentboptfieldvaluetype <- do+    alignmentboptfieldvaluetypep <-+      DABL.take 1+    -- Parse BOPT value type of the alignment section.+    case (alignmentboptfieldvaluetypep =~ [re|[cCsSiIf]|]) of+      False ->+        fail $+          show BAM_V1_6_Read_Error_Alignment_BOPT_Value_Type_Incorrect_Format+      True  ->+        -- BOPT value type is in the accepted format.+        return alignmentboptfieldvaluetypep+  alignmentboptfieldcount <-+    DABL.take 4+  case (DBC8.unpack alignmentboptfieldvaluetype) of+    "c" -> do+      alignmentboptfieldvaluedata <- do+        alignmentboptfieldvaluedatap <-+          DABL.take $+            ( fromIntegral       $+                word8sToWord32LE $+                  DB.unpack alignmentboptfieldcount+            ) * 1+        -- Parse BOPT value data of the alignment section.+        case (alignmentboptfieldvaluedatap =~ [re|([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)*|]) of+          False ->+            fail $+              show BAM_V1_6_Read_Error_Alignment_BOPT_Value_Data_Incorrect_Format+          True  ->+            -- BOPT value data is in the accepted format.+            return alignmentboptfieldvaluedatap +      return BAM_V1_6_BAM_Alignment_OptionalFields_BOPT+               { bam_v1_6_bam_alignment_optionalfields_bopt_int8   = Just BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8+                                                                            { bam_v1_6_bam_alignment_optionalfields_bopt_int8_tag   = alignmentboptfieldtag+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_int8_type  = alignmentboptfieldvaluetype+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_int8_count = word8sToWord32LE $+                                                                                                                                        DB.unpack alignmentboptfieldcount+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_int8_value = DSeq.fromList                      $+                                                                                                                                        map (word8sToInt8LE . DB.unpack) $+                                                                                                                                          splitByteString 1+                                                                                                                                                          alignmentboptfieldvaluedata+                                                                            }+               , bam_v1_6_bam_alignment_optionalfields_bopt_word8  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_int16  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word16 = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_int32  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word32 = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_float  = Nothing+               }+    "C" -> do+      alignmentboptfieldvaluedata <- do+        alignmentboptfieldvaluedatap <-+          DABL.take $+            ( fromIntegral       $+                word8sToWord32LE $+                  DB.unpack alignmentboptfieldcount+            ) * 1+        -- Parse BOPT value data of the alignment section.+        case (alignmentboptfieldvaluedatap =~ [re|([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)*|]) of+          False ->+            fail $+              show BAM_V1_6_Read_Error_Alignment_BOPT_Value_Data_Incorrect_Format+          True  ->+            -- BOPT value data is in the accepted format.+            return alignmentboptfieldvaluedatap+      return BAM_V1_6_BAM_Alignment_OptionalFields_BOPT+               { bam_v1_6_bam_alignment_optionalfields_bopt_int8   = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word8  = Just BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8+                                                                            { bam_v1_6_bam_alignment_optionalfields_bopt_word8_tag   = alignmentboptfieldtag+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_word8_type  = alignmentboptfieldvaluetype+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_word8_count = word8sToWord32LE $+                                                                                                                                         DB.unpack alignmentboptfieldcount+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_word8_value = DSeq.fromList                       $+                                                                                                                                         map (word8sToWord8LE . DB.unpack) $+                                                                                                                                           splitByteString 1+                                                                                                                                                           alignmentboptfieldvaluedata+                                                                            }+               , bam_v1_6_bam_alignment_optionalfields_bopt_int16  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word16 = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_int32  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word32 = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_float  = Nothing+               }+    "s" -> do+      alignmentboptfieldvaluedata <- do+        alignmentboptfieldvaluedatap <-+          DABL.take $+            ( fromIntegral       $+                word8sToWord32LE $+                  DB.unpack alignmentboptfieldcount+            ) * 2+        -- Parse BOPT value data of the alignment section.+        case (alignmentboptfieldvaluedatap =~ [re|([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)*|]) of+          False ->+            fail $+              show BAM_V1_6_Read_Error_Alignment_BOPT_Value_Data_Incorrect_Format+          True  ->+            -- BOPT value data is in the accepted format.+            return alignmentboptfieldvaluedatap+      return BAM_V1_6_BAM_Alignment_OptionalFields_BOPT+               { bam_v1_6_bam_alignment_optionalfields_bopt_int8   = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word8  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_int16  = Just BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16+                                                                            { bam_v1_6_bam_alignment_optionalfields_bopt_int16_tag   = alignmentboptfieldtag+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_int16_type  = alignmentboptfieldvaluetype+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_int16_count = word8sToWord32LE $+                                                                                                                                         DB.unpack alignmentboptfieldcount+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_int16_value = DSeq.fromList                       $+                                                                                                                                         map (word8sToInt16LE . DB.unpack) $ +                                                                                                                                           splitByteString 2+                                                                                                                                                           alignmentboptfieldvaluedata+                                                                            }+               , bam_v1_6_bam_alignment_optionalfields_bopt_word16 = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_int32  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word32 = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_float  = Nothing+               }+    "S" -> do+      alignmentboptfieldvaluedata <- do+        alignmentboptfieldvaluedatap <-+          DABL.take $+            ( fromIntegral       $+                word8sToWord32LE $+                  DB.unpack alignmentboptfieldcount+            ) * 2+        -- Parse BOPT value data of the alignment section.+        case (alignmentboptfieldvaluedatap =~ [re|([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)*|]) of+          False ->+            fail $+              show BAM_V1_6_Read_Error_Alignment_BOPT_Value_Data_Incorrect_Format+          True  ->+            -- BOPT value data is in the accepted format.+            return alignmentboptfieldvaluedatap+      return BAM_V1_6_BAM_Alignment_OptionalFields_BOPT+               { bam_v1_6_bam_alignment_optionalfields_bopt_int8   = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word8  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_int16  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word16 = Just BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16+                                                                            { bam_v1_6_bam_alignment_optionalfields_bopt_word16_tag   = alignmentboptfieldtag+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_word16_type  = alignmentboptfieldvaluetype+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_word16_count = word8sToWord32LE $+                                                                                                                                          DB.unpack alignmentboptfieldcount+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_word16_value = DSeq.fromList                        $+                                                                                                                                          map (word8sToWord16LE . DB.unpack) $+                                                                                                                                            splitByteString 2+                                                                                                                                                            alignmentboptfieldvaluedata+                                                                            }+               , bam_v1_6_bam_alignment_optionalfields_bopt_int32  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word32 = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_float  = Nothing+               }+    "i" -> do+      alignmentboptfieldvaluedata <- do+        alignmentboptfieldvaluedatap <-+          DABL.take $+            ( fromIntegral       $+                word8sToWord32LE $+                  DB.unpack alignmentboptfieldcount+            ) * 4+        -- Parse BOPT value data of the alignment section.+        case (alignmentboptfieldvaluedatap =~ [re|([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)*|]) of+          False ->+            fail $+              show BAM_V1_6_Read_Error_Alignment_BOPT_Value_Data_Incorrect_Format+          True  ->+            -- BOPT value data is in the accepted format.+            return alignmentboptfieldvaluedatap+      return BAM_V1_6_BAM_Alignment_OptionalFields_BOPT+               { bam_v1_6_bam_alignment_optionalfields_bopt_int8   = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word8  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_int16  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word16 = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_int32  = Just BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32+                                                                            { bam_v1_6_bam_alignment_optionalfields_bopt_int32_tag   = alignmentboptfieldtag+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_int32_type  = alignmentboptfieldvaluetype+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_int32_count = word8sToWord32LE $+                                                                                                                                         DB.unpack alignmentboptfieldcount+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_int32_value = DSeq.fromList                       $+                                                                                                                                         map (word8sToInt32LE . DB.unpack) $+                                                                                                                                           splitByteString 4+                                                                                                                                                           alignmentboptfieldvaluedata+                                                                            }+               , bam_v1_6_bam_alignment_optionalfields_bopt_word32 = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_float  = Nothing+               }+    "I" -> do+      alignmentboptfieldvaluedata <- do+        alignmentboptfieldvaluedatap <-+          DABL.take $+            ( fromIntegral       $+                word8sToWord32LE $+                  DB.unpack alignmentboptfieldcount+            ) * 4+        -- Parse BOPT value data of the alignment section.+        case (alignmentboptfieldvaluedatap =~ [re|([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)*|]) of+          False ->+            fail $+              show BAM_V1_6_Read_Error_Alignment_BOPT_Value_Data_Incorrect_Format+          True  ->+            -- BOPT value data is in the accepted format.+            return alignmentboptfieldvaluedatap+      return BAM_V1_6_BAM_Alignment_OptionalFields_BOPT+               { bam_v1_6_bam_alignment_optionalfields_bopt_int8   = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word8  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_int16  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word16 = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_int32  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word32 = Just BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32+                                                                            { bam_v1_6_bam_alignment_optionalfields_bopt_word32_tag   = alignmentboptfieldtag+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_word32_type  = alignmentboptfieldvaluetype+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_word32_count = word8sToWord32LE $+                                                                                                                                          DB.unpack alignmentboptfieldcount+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_word32_value = DSeq.fromList                        $+                                                                                                                                          map (word8sToWord32LE . DB.unpack) $+                                                                                                                                            splitByteString 4+                                                                                                                                                            alignmentboptfieldvaluedata+                                                                            }+               , bam_v1_6_bam_alignment_optionalfields_bopt_float  = Nothing+               }+    "f" -> do+      alignmentboptfieldvaluedata <- do+        alignmentboptfieldvaluedatap <-+          DABL.take $+            ( fromIntegral       $+                word8sToWord32LE $+                  DB.unpack alignmentboptfieldcount+            ) * 4+        -- Parse BOPT value data of the alignment section.+        case (alignmentboptfieldvaluedatap =~ [re|([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)*|]) of+          False ->+            fail $+              show BAM_V1_6_Read_Error_Alignment_BOPT_Value_Data_Incorrect_Format+          True  ->+            -- BOPT value data is in the accepted format.+            return alignmentboptfieldvaluedatap+      return BAM_V1_6_BAM_Alignment_OptionalFields_BOPT+               { bam_v1_6_bam_alignment_optionalfields_bopt_int8   = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word8  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_int16  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word16 = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_int32  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word32 = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_float  = Just BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float+                                                                            { bam_v1_6_bam_alignment_optionalfields_bopt_float_tag   = alignmentboptfieldtag+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_float_type  = alignmentboptfieldvaluetype+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_float_count = word8sToWord32LE $+                                                                                                                                         DB.unpack alignmentboptfieldcount+                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_float_value = DSeq.fromList             $+                                                                                                                                         map bytestringToFloatLE $+                                                                                                                                           splitByteString 4+                                                                                                                                                           alignmentboptfieldvaluedata+                                                                            }+               }+    _   ->+      return BAM_V1_6_BAM_Alignment_OptionalFields_BOPT+               { bam_v1_6_bam_alignment_optionalfields_bopt_int8   = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word8  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_int16  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word16 = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_int32  = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_word32 = Nothing+               , bam_v1_6_bam_alignment_optionalfields_bopt_float  = Nothing+               }

@@ -0,0 +1,84 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BigCOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BigCOPT ( -- * BAM_V1_6_BAM parser - alignment section - bigcopt field +                                                                              parse_BAM_V1_6_BAM_Alignment_OptionalFields_BigCOPT+                                                                            ) where++import           Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BigCOPT+import           Data.BAM.Version1_6.Internal+import           Data.BAM.Version1_6.Read.Error++import           Data.ByteString                 as DB+import           Data.Attoparsec.ByteString.Lazy as DABL+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the optional bigcopt field of alignment section of the BAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_BAM_V1_6_BAM_Alignment_OptionalFields_BigCOPT :: Parser BAM_V1_6_BAM_Alignment_OptionalFields_BigCOPT+parse_BAM_V1_6_BAM_Alignment_OptionalFields_BigCOPT = do+  alignmentbigcoptfieldtag <- do+    alignmentbigcoptfieldtagp <-+      DABL.take 2+    -- Parse BigCOPT tag of the alignment section.+    case (alignmentbigcoptfieldtagp =~ [re|[A-Za-z][A-Za-z0-9]|]) of+      False ->+        fail $ show BAM_V1_6_Read_Error_Alignment_BigCOPT_Tag_Incorrect_Format+      True  ->+        -- BigCOPT tag is in the accepted format. +        return alignmentbigcoptfieldtagp+  _ <- do+    alignmentbigcoptfieldtypep <-+      DABL.take 1+    -- Parse BigCOPT type of the alignment section.+    case (alignmentbigcoptfieldtypep =~ [re|[C]|]) of+      False ->+        fail $ show BAM_V1_6_Read_Error_Alignment_BigCOPT_Type_Incorrect_Format+      True  ->+        -- BigCOPT type is in the accepted format.+        return ()+  alignmentbigcoptfieldvalue <-+    DABL.take 1 +  return BAM_V1_6_BAM_Alignment_OptionalFields_BigCOPT+           { bam_v1_6_bam_alignment_optionalfields_bigcopt_tag   = alignmentbigcoptfieldtag+           , bam_v1_6_bam_alignment_optionalfields_bigcopt_value = word8sToWord8LE $+                                                                     DB.unpack alignmentbigcoptfieldvalue+           }

@@ -0,0 +1,84 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BigIOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BigIOPT ( -- * BAM_V1_6_BAM parser - alignment section - bigiopt field +                                                                              parse_BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT+                                                                            ) where++import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BigIOPT+import Data.BAM.Version1_6.Internal+import Data.BAM.Version1_6.Read.Error++import Data.ByteString                 as DB+import Data.Attoparsec.ByteString.Lazy as DABL+import Text.Regex.PCRE.Heavy++-- | Defines a parser for the optional bigiopt field of alignment section of the BAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT :: Parser BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT+parse_BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT = do+  alignmentbigioptfieldtag <- do+    alignmentbigioptfieldtagp <-+      DABL.take 2+    -- Parse BigIOPT tag of the alignment section.+    case (alignmentbigioptfieldtagp =~ [re|[A-Za-z][A-Za-z0-9]|]) of+      False ->+        fail $ show BAM_V1_6_Read_Error_Alignment_BigIOPT_Tag_Incorrect_Format+      True  ->+        -- BigIOPT tag is in the accepted format. +        return alignmentbigioptfieldtagp+  _ <- do+    alignmentbigioptfieldtypep <-+      DABL.take 1+    -- Parse BigIOPT type of the alignment section.+    case (alignmentbigioptfieldtypep =~ [re|[I]|]) of+      False ->+        fail $ show BAM_V1_6_Read_Error_Alignment_BigIOPT_Type_Incorrect_Format+      True  ->+        -- BigIOPT type is in the accepted format.+        return ()+  alignmentbigioptfieldvalue <-+    DABL.take 4+  return BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT+           { bam_v1_6_bam_alignment_optionalfields_bigiopt_tag   = alignmentbigioptfieldtag+           , bam_v1_6_bam_alignment_optionalfields_bigiopt_value = word8sToWord32LE $+                                                                     DB.unpack alignmentbigioptfieldvalue+           }

@@ -0,0 +1,84 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BigSOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BigSOPT ( -- * BAM_V1_6_BAM parser - alignment section - bigsopt field +                                                                              parse_BAM_V1_6_BAM_Alignment_OptionalFields_BigSOPT+                                                                            ) where++import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BigSOPT+import Data.BAM.Version1_6.Internal+import Data.BAM.Version1_6.Read.Error++import Data.ByteString                  as DB+import Data.Attoparsec.ByteString.Lazy  as DABL+import Text.Regex.PCRE.Heavy++-- | Defines a parser for the optional bigsopt field of alignment section of the BAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_BAM_V1_6_BAM_Alignment_OptionalFields_BigSOPT :: Parser BAM_V1_6_BAM_Alignment_OptionalFields_BigSOPT+parse_BAM_V1_6_BAM_Alignment_OptionalFields_BigSOPT = do+  alignmentbigsoptfieldtag <- do+    alignmentbigsoptfieldtagp <-+      DABL.take 2+    -- Parse BigSOPT tag of the alignment section.+    case (alignmentbigsoptfieldtagp =~ [re|[A-Za-z][A-Za-z0-9]|]) of+      False ->+        fail $ show BAM_V1_6_Read_Error_Alignment_BigSOPT_Tag_Incorrect_Format+      True  ->+        -- BigSOPT tag is in the accepted format. +        return alignmentbigsoptfieldtagp+  _ <- do+    alignmentbigsoptfieldtypep <-+      DABL.take 1+    -- Parse BigSOPT type of the alignment section.+    case (alignmentbigsoptfieldtypep =~ [re|[S]|]) of+      False ->+        fail $ show BAM_V1_6_Read_Error_Alignment_BigSOPT_Type_Incorrect_Format+      True  ->+        -- BigSOPT type is in the accepted format.+        return ()+  alignmentbigsoptfieldvalue <-+    DABL.take 2+  return BAM_V1_6_BAM_Alignment_OptionalFields_BigSOPT+           { bam_v1_6_bam_alignment_optionalfields_bigsopt_tag   = alignmentbigsoptfieldtag+           , bam_v1_6_bam_alignment_optionalfields_bigsopt_value = word8sToWord16LE $+                                                                     DB.unpack alignmentbigsoptfieldvalue+           }

@@ -0,0 +1,95 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.FOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.FOPT ( -- * BAM_V1_6 parser - alignment section - fopt field +                                                                           parse_BAM_V1_6_BAM_Alignment_OptionalFields_FOPT+                                                                         ) where++import           Data.BAM.Version1_6.BAM.Alignment.OptionalFields.FOPT+import           Data.BAM.Version1_6.Internal+import           Data.BAM.Version1_6.Read.Error++import           Data.ByteString                 as DB+import           Data.Attoparsec.ByteString.Lazy as DABL+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the optional fopt field of alignment section of the BAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_BAM_V1_6_BAM_Alignment_OptionalFields_FOPT :: Parser BAM_V1_6_BAM_Alignment_OptionalFields_FOPT+parse_BAM_V1_6_BAM_Alignment_OptionalFields_FOPT = do+  alignmentfoptfieldtag <- do+    alignmentfoptfieldtagp <-+      DABL.take 2+    -- Parse FOPT tag of the alignment section.+    case (alignmentfoptfieldtagp =~ [re|[A-Za-z][A-Za-z0-9]|]) of+      False ->+        fail $+          show BAM_V1_6_Read_Error_Alignment_FOPT_Tag_Incorrect_Format+      True  ->+        -- FOPT tag is in the accepted format. +        return alignmentfoptfieldtagp+  _ <- do+    alignmentfoptfieldtypep <-+      DABL.take 1+    -- Parse FOPT type of the alignment section.+    case (alignmentfoptfieldtypep =~ [re|[f]|]) of+      False ->+        fail $+          show BAM_V1_6_Read_Error_Alignment_FOPT_Type_Incorrect_Format+      True  ->+        -- FOPT type is in the accepted format.+        return ()+  alignmentfoptfieldvalue <- do+    alignmentfoptfieldvaluep <-+      DABL.take 4+    -- Parse FOPT value of the alignment section.+    case (alignmentfoptfieldvaluep =~ [re|[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?|]) of+      False ->+        fail $+          show BAM_V1_6_Read_Error_Alignment_FOPT_Value_Incorrect_Format+      True  ->+        -- FOPT value is in the accepted format.+        return alignmentfoptfieldvaluep+  return BAM_V1_6_BAM_Alignment_OptionalFields_FOPT+           { bam_v1_6_bam_alignment_optionalfields_fopt_tag   = alignmentfoptfieldtag+           , bam_v1_6_bam_alignment_optionalfields_fopt_value = word8sToWord32LE $+                                                                  DB.unpack alignmentfoptfieldvalue+           }

@@ -0,0 +1,110 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.HOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.HOPT ( -- * BAM_V1_6 parser - alignment section - hopt field +                                                                           parse_BAM_V1_6_BAM_Alignment_OptionalFields_HOPT+                                                                         ) where++import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.HOPT+import Data.BAM.Version1_6.Internal+import Data.BAM.Version1_6.Read.Error++import Data.ByteString.Base16            as DBB16+import Data.Base16.Types                 as DBB16T+import Data.Attoparsec.ByteString.Lazy   as DABL+import Data.Sequence                     as DSeq+import Text.Regex.PCRE.Heavy++-- | Defines a parser for the optional hopt field of alignment section of the BAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_BAM_V1_6_BAM_Alignment_OptionalFields_HOPT :: Parser BAM_V1_6_BAM_Alignment_OptionalFields_HOPT+parse_BAM_V1_6_BAM_Alignment_OptionalFields_HOPT = do+  alignmenthoptfieldtag <- do+    alignmenthoptfieldtagp <-+      DABL.take 2+    -- Parse HOPT tag of the alignment section.+    case (alignmenthoptfieldtagp =~ [re|[A-Za-z][A-Za-z0-9]|]) of+      False ->+        fail $+          show BAM_V1_6_Read_Error_Alignment_HOPT_Tag_Incorrect_Format+      True  ->+        -- HOPT tag is in the accepted format. +        return alignmenthoptfieldtagp+  _ <- do+    alignmenthoptfieldtypep <-+      DABL.take 1+    -- Parse HOPT type of the alignment section.+    case (alignmenthoptfieldtypep =~ [re|[H]|]) of+      False ->+        fail $+          show BAM_V1_6_Read_Error_Alignment_HOPT_Type_Incorrect_Format+      True  ->+        -- HOPT type is in the accepted format.+        return ()+  alignmenthoptfieldvalue <- do+    alignmenthoptfieldvaluep <-+      DABL.takeTill (\x -> x == 0x00)+    -- Parse HOPT value of the alignment section.+    case (alignmenthoptfieldvaluep =~ [re|([0-9A-F][0-9A-F])*|]) of+      False ->+        fail $+          show BAM_V1_6_Read_Error_Alignment_HOPT_Value_Incorrect_Format+      True  ->+        -- HOPT value is in the accepted format.+        return $+          Prelude.map (\currenthexvalue -> do+                         case (DBB16.isBase16 alignmenthoptfieldvaluep) of+                           False ->+                             error $+                               show BAM_V1_6_Read_Error_Alignment_HOPT_Value_Incorrect_Format+                           True  ->+                             DBB16.decodeBase16    $+                               DBB16T.assertBase16 currenthexvalue+                      ) $+          ( splitByteString 2+                            alignmenthoptfieldvaluep+          )+  _ <-+    DABL.take 1+  return BAM_V1_6_BAM_Alignment_OptionalFields_HOPT+           { bam_v1_6_bam_alignment_optionalfields_hopt_tag   = alignmenthoptfieldtag+           , bam_v1_6_bam_alignment_optionalfields_hopt_value = DSeq.fromList alignmenthoptfieldvalue+           }

@@ -0,0 +1,84 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.SmallCOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.SmallCOPT ( -- * BAM_V1_6_BAM parser - alignment section - smallcopt field +                                                                                parse_BAM_V1_6_BAM_Alignment_OptionalFields_SmallCOPT+                                                                              ) where++import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.SmallCOPT+import Data.BAM.Version1_6.Internal+import Data.BAM.Version1_6.Read.Error++import Data.Attoparsec.ByteString.Lazy as DABL+import Data.ByteString                 as DB+import Text.Regex.PCRE.Heavy++-- | Defines a parser for the optional smallcopt field of alignment section of the BAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_BAM_V1_6_BAM_Alignment_OptionalFields_SmallCOPT :: Parser BAM_V1_6_BAM_Alignment_OptionalFields_SmallCOPT+parse_BAM_V1_6_BAM_Alignment_OptionalFields_SmallCOPT = do+  alignmentsmallcoptfieldtag <- do+    alignmentsmallcoptfieldtagp <-+      DABL.take 2+    -- Parse SmallCOPT tag of the alignment section.+    case (alignmentsmallcoptfieldtagp =~ [re|[A-Za-z][A-Za-z0-9]|]) of+      False ->+        fail $ show BAM_V1_6_Read_Error_Alignment_SmallCOPT_Tag_Incorrect_Format+      True  ->+        -- SmallCOPT tag is in the accepted format. +        return alignmentsmallcoptfieldtagp+  _ <- do+    alignmentsmallcoptfieldtypep <-+      DABL.take 1+    -- Parse SmallCOPT type of the alignment section.+    case (alignmentsmallcoptfieldtypep =~ [re|[c]|]) of+      False ->+        fail $ show BAM_V1_6_Read_Error_Alignment_SmallCOPT_Type_Incorrect_Format+      True  ->+        -- SmallCOPT type is in the accepted format.+        return ()+  alignmentsmallcoptfieldvalue <-+    DABL.take 1 +  return BAM_V1_6_BAM_Alignment_OptionalFields_SmallCOPT+           { bam_v1_6_bam_alignment_optionalfields_smallcopt_tag   = alignmentsmallcoptfieldtag+           , bam_v1_6_bam_alignment_optionalfields_smallcopt_value = word8sToInt8LE $+                                                                       DB.unpack alignmentsmallcoptfieldvalue+           }

@@ -0,0 +1,84 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.SmallIOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.SmallIOPT ( -- * BAM_V1_6_BAM parser - alignment section - smalliopt field +                                                                                parse_BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT+                                                                              ) where++import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.SmallIOPT+import Data.BAM.Version1_6.Internal+import Data.BAM.Version1_6.Read.Error++import Data.ByteString                 as DB+import Data.Attoparsec.ByteString.Lazy as DABL+import Text.Regex.PCRE.Heavy++-- | Defines a parser for the optional smalliopt field of alignment section of the BAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT :: Parser BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT+parse_BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT = do+  alignmentsmallioptfieldtag <- do+    alignmentsmallioptfieldtagp <-+      DABL.take 2+    -- Parse SmallIOPT tag of the alignment section.+    case (alignmentsmallioptfieldtagp =~ [re|[A-Za-z][A-Za-z0-9]|]) of+      False ->+        fail $ show BAM_V1_6_Read_Error_Alignment_SmallIOPT_Tag_Incorrect_Format+      True  ->+        -- SmallIOPT tag is in the accepted format. +        return alignmentsmallioptfieldtagp+  _ <- do+    alignmentsmallioptfieldtypep <-+      DABL.take 1+    -- Parse SmallIOPT type of the alignment section.+    case (alignmentsmallioptfieldtypep =~ [re|[i]|]) of+      False ->+        fail $ show BAM_V1_6_Read_Error_Alignment_SmallIOPT_Type_Incorrect_Format+      True  ->+        -- SmallIOPT type is in the accepted format.+        return ()+  alignmentsmallioptfieldvalue <-+    DABL.take 4+  return BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT+           { bam_v1_6_bam_alignment_optionalfields_smalliopt_tag   = alignmentsmallioptfieldtag+           , bam_v1_6_bam_alignment_optionalfields_smalliopt_value = word8sToInt32LE $+                                                                       DB.unpack alignmentsmallioptfieldvalue+           }

@@ -0,0 +1,84 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.SmallSOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.SmallSOPT ( -- * BAM_V1_6_BAM parser - alignment section - smallsopt field +                                                                                parse_BAM_V1_6_BAM_Alignment_OptionalFields_SmallSOPT+                                                                              ) where++import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.SmallSOPT+import Data.BAM.Version1_6.Internal+import Data.BAM.Version1_6.Read.Error++import Data.ByteString                 as DB+import Data.Attoparsec.ByteString.Lazy as DABL+import Text.Regex.PCRE.Heavy++-- | Defines a parser for the optional smallsopt field of alignment section of the BAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_BAM_V1_6_BAM_Alignment_OptionalFields_SmallSOPT :: Parser BAM_V1_6_BAM_Alignment_OptionalFields_SmallSOPT+parse_BAM_V1_6_BAM_Alignment_OptionalFields_SmallSOPT = do+  alignmentsmallsoptfieldtag <- do+    alignmentsmallsoptfieldtagp <-+      DABL.take 2+    -- Parse SmallSOPT tag of the alignment section.+    case (alignmentsmallsoptfieldtagp =~ [re|[A-Za-z][A-Za-z0-9]|]) of+      False ->+        fail $ show BAM_V1_6_Read_Error_Alignment_SmallSOPT_Tag_Incorrect_Format+      True  ->+        -- SmallSOPT tag is in the accepted format. +        return alignmentsmallsoptfieldtagp+  _ <- do+    alignmentsmallsoptfieldtypep <-+      DABL.take 1+    -- Parse SmallSOPT type of the alignment section.+    case (alignmentsmallsoptfieldtypep =~ [re|[s]|]) of+      False ->+        fail $ show BAM_V1_6_Read_Error_Alignment_SmallSOPT_Type_Incorrect_Format+      True  ->+        -- SmallSOPT type is in the accepted format.+        return ()+  alignmentsmallsoptfieldvalue <-+    DABL.take 2+  return BAM_V1_6_BAM_Alignment_OptionalFields_SmallSOPT+           { bam_v1_6_bam_alignment_optionalfields_smallsopt_tag   = alignmentsmallsoptfieldtag+           , bam_v1_6_bam_alignment_optionalfields_smallsopt_value = word8sToInt16LE $+                                                                       DB.unpack alignmentsmallsoptfieldvalue+           }

@@ -0,0 +1,97 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.ZOPT+-- Copyright   :  (c) Matthew Mosior 2024+-- License     :  BSD-style+-- Maintainer  :  mattm.github@gmail.com+-- Portability :  portable+--+-- = WARNING+--+-- This module is considered __internal__.+--+-- The Package Versioning Policy __does not apply__.+--+-- The contents of this module may change __in any way whatsoever__+-- and __without any warning__ between minor versions of this package.+--+-- Authors importing this library are expected to track development+-- closely.+--+-- All credit goes to the author(s)/maintainer(s) of the+-- [containers](https://hackage.haskell.org/package/containers) library+-- for the above warning text.+--+-- = Description+--+-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.++module Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.ZOPT ( -- * BAM_V1_6 parser - alignment section - zopt field +                                                                           parse_BAM_V1_6_BAM_Alignment_OptionalFields_ZOPT+                                                                         ) where++import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.ZOPT+import Data.BAM.Version1_6.Read.Error++import Data.ByteString                 as DB+import Data.Attoparsec.ByteString.Lazy as DABL+import Data.Sequence                   as DSeq+import Text.Regex.PCRE.Heavy++-- | Defines a parser for the optional zopt field of alignment section of the BAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_BAM_V1_6_BAM_Alignment_OptionalFields_ZOPT :: Parser BAM_V1_6_BAM_Alignment_OptionalFields_ZOPT+parse_BAM_V1_6_BAM_Alignment_OptionalFields_ZOPT = do+  alignmentzoptfieldtag <- do+    alignmentzoptfieldtagp <-+      DABL.take 2+    -- Parse ZOPT tag of the alignment section.+    case (alignmentzoptfieldtagp =~ [re|[A-Za-z][A-Za-z0-9]|]) of+      False ->+        fail $+          show BAM_V1_6_Read_Error_Alignment_ZOPT_Tag_Incorrect_Format+      True  ->+        -- ZOPT tag is in the accepted format. +        return alignmentzoptfieldtagp+  _ <- do+    alignmentzoptfieldtypep <-+      DABL.take 1+    -- Parse ZOPT type of the alignment section.+    case (alignmentzoptfieldtypep =~ [re|[Z]|]) of+      False ->+        fail $+          show BAM_V1_6_Read_Error_Alignment_ZOPT_Type_Incorrect_Format+      True  ->+        -- ZOPT type is in the accepted format.+        return ()+  alignmentzoptfieldvalue <- do+    alignmentzoptfieldvaluep <-+      DABL.takeTill (\x -> x == 0x00)+    -- Parse ZOPT value of the alignment section.+    case (alignmentzoptfieldvaluep =~ [re|[ !-~]*|]) of+      False ->+        fail $+          show BAM_V1_6_Read_Error_Alignment_ZOPT_Value_Incorrect_Format+      True  ->+        -- ZOPT value is in the accepted format.+        return alignmentzoptfieldvaluep+  _ <-+    DABL.take 1+  return BAM_V1_6_BAM_Alignment_OptionalFields_ZOPT+           { bam_v1_6_bam_alignment_optionalfields_zopt_tag   = alignmentzoptfieldtag+           , bam_v1_6_bam_alignment_optionalfields_zopt_value = DSeq.fromList $+                                                                  DB.unpack alignmentzoptfieldvalue+           }