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hs-samtools (empty) → 0.5.0.2

raw patch · 62 files changed

+5903/−0 lines, 62 filesdep +asciidep +attoparsecdep +base

Dependencies added: ascii, attoparsec, base, bitvec, bytestring, containers, crypton, generic-deriving, hs-samtools, pcre-heavy, regex-tdfa, streamly, streamly-bytestring, streamly-core

Files

+ CHANGELOG.md view
@@ -0,0 +1,62 @@+# Revision history for hs-samtools++## 0.1.0.0 -- 2023-08-12++* First version. Released on an unsuspecting world.++## 0.1.0.1 -- 2023-08-12++* Added package bounds for ascii, bytestring, containers, crypton, and flatparse.++## 0.2.0.0 -- 2023-08-13++* Added Eq, Generic, Show and Typeable classes/instances to Data.SAM.Version1_6.Header.CO, Data.SAM.Version1_6.Header.HD, Data.SAM.Version1_6.Header.PG, Data.SAM.Version1_6.Header.RG, Data.SAM.Version1_6.Header.SQ data types.++## 0.2.0.1 -- 2023-08-13++* Removed unnecessary Eq and Show instance comments.++## 0.3.0.0 -- 2023-08-14++* Created Data.SAM.Version1_6.Alignment and Data.SAM.Version1_6.Header (re-exports).+* Renamed Data.SAM.Version1_6.Internal to Data.SAM.Version1_6.Base.+* Added Data.SAM.Version1_6.Alignment.Base and Data.SAM.Version1_6.Alignment.BOPT.++## 0.3.1.0 -- 2023-08-14++* Added SAM_V1_6_Alignment_BOPT_Float(..) to Data.SAM.Version1_6.Alignment.BOPT.++## 0.4.0.0 -- 2023-08-16++* Added comments to SAM_V1_6_Alignment(..) in Data.SAM.Version1_6.Alignment.Base.+* Changed sam_v1_6_alignment_flag (SAM_V1_6_Alignment(..)) from Int to Vector Bit in Data.SAM.Version1_6.Alignment.Base.++## 0.4.0.1 -- 2023-08-16++* Fixed comments to SAM_V1_6_Alignment(..) in Data.SAM.Version1_6.Alignment.Base.++## 0.4.0.2 -- 2023-08-16++* Fixed comments to SAM_V1_6_Alignment(..) in Data.SAM.Version1_6.Alignment.Base.++## 0.4.0.3 -- 2023-08-16++* Fixed comments to SAM_V1_6_Alignment(..) in Data.SAM.Version1_6.Alignment.Base.++## 0.4.0.4 -- 2023-08-17++* Added comment to sam_v1_6_alignment (SAM_V1_6(..)) in Data.SAM.Version1_6.Base.++## 0.5.0.0 -- 2023-09-01++* Added attoparsec parsers for alignment and header section of SAM_V1_6(..).+* Added attoparsec parser for SAM_V1_6(..).+* Added SAM_V1_6(..) reading functionality.++## 0.5.0.1 -- 2023-09-01++* Fix documentation for readSAM_V1_6.++## 0.5.0.2 -- 2023-09-01++* Fix/update lots of documentation across entire codebase.
+ LICENSE view
@@ -0,0 +1,30 @@+Copyright (c) 2023, Matthew Mosior++All rights reserved.++Redistribution and use in source and binary forms, with or without+modification, are permitted provided that the following conditions are met:++    * Redistributions of source code must retain the above copyright+      notice, this list of conditions and the following disclaimer.++    * Redistributions in binary form must reproduce the above+      copyright notice, this list of conditions and the following+      disclaimer in the documentation and/or other materials provided+      with the distribution.++    * Neither the name of Matthew Mosior nor the names of other+      contributors may be used to endorse or promote products derived+      from this software without specific prior written permission.++THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ hs-samtools.cabal view
@@ -0,0 +1,173 @@+cabal-version:      3.0+-- The cabal-version field refers to the version of the .cabal specification,+-- and can be different from the cabal-install (the tool) version and the+-- Cabal (the library) version you are using. As such, the Cabal (the library)+-- version used must be equal or greater than the version stated in this field.+-- Starting from the specification version 2.2, the cabal-version field must be+-- the first thing in the cabal file.++-- Initial package description 'hs-samtools' generated by+-- 'cabal init'. For further documentation, see:+--   http://haskell.org/cabal/users-guide/+--+-- The name of the package.+name:               hs-samtools++-- The package version.+-- See the Haskell package versioning policy (PVP) for standards+-- guiding when and how versions should be incremented.+-- https://pvp.haskell.org+-- PVP summary:     +-+------- breaking API changes+--                  | | +----- non-breaking API additions+--                  | | | +--- code changes with no API change+version:            0.5.0.2++-- A short (one-line) description of the package.+synopsis: Read and write SAM, BAM, and CRAM files.++-- A longer description of the package.+description: A SAM, BAM, and CRAM file decoder/encoded along with various related functionality associated with these file formats.++-- The license under which the package is released.+license:            BSD-3-Clause++-- The file containing the license text.+license-file:       LICENSE++-- The package author(s).+author:             Matthew Mosior++-- An email address to which users can send suggestions, bug reports, and patches.+maintainer:         mattm.github@gmail.com++-- A copyright notice.+-- copyright:+category:           Bioinformatics+build-type:         Simple++-- Extra doc files to be distributed with the package, such as a CHANGELOG or a README.+extra-doc-files:    CHANGELOG.md++-- Extra source files to be distributed with the package, such as examples, or a tutorial module.+-- extra-source-files:++common warnings+    ghc-options: -Wall++library+    -- Import common warning flags.+    import:           warnings++    -- Modules exported by the library.+    exposed-modules: Data.SAM.Version1_6.Base,+                     Data.SAM.Version1_6.Alignment,+                     Data.SAM.Version1_6.Alignment.Base,+                     Data.SAM.Version1_6.Alignment.BOPT,+                     Data.SAM.Version1_6.Header, +                     Data.SAM.Version1_6.Header.CO,+                     Data.SAM.Version1_6.Header.HD,+                     Data.SAM.Version1_6.Header.PG,+                     Data.SAM.Version1_6.Header.RG,+                     Data.SAM.Version1_6.Header.SQ,+                     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.Header.HD.Base,+                     Data.SAM.Version1_6.Read.Parser.Header.HD.VN,+                     Data.SAM.Version1_6.Read.Parser.Header.HD.SO,+                     Data.SAM.Version1_6.Read.Parser.Header.HD.GO,+                     Data.SAM.Version1_6.Read.Parser.Header.HD.SS,+                     Data.SAM.Version1_6.Read.Parser.Header.SQ.Base,+                     Data.SAM.Version1_6.Read.Parser.Header.SQ.SN,+                     Data.SAM.Version1_6.Read.Parser.Header.SQ.LN,+                     Data.SAM.Version1_6.Read.Parser.Header.SQ.AH,+                     Data.SAM.Version1_6.Read.Parser.Header.SQ.AN,+                     Data.SAM.Version1_6.Read.Parser.Header.SQ.AS,+                     Data.SAM.Version1_6.Read.Parser.Header.SQ.DS,+                     Data.SAM.Version1_6.Read.Parser.Header.SQ.M5,+                     Data.SAM.Version1_6.Read.Parser.Header.SQ.SP,+                     Data.SAM.Version1_6.Read.Parser.Header.SQ.TP,+                     Data.SAM.Version1_6.Read.Parser.Header.SQ.UR,+                     Data.SAM.Version1_6.Read.Parser.Header.RG.Base,+                     Data.SAM.Version1_6.Read.Parser.Header.RG.ID,+                     Data.SAM.Version1_6.Read.Parser.Header.RG.BC,+                     Data.SAM.Version1_6.Read.Parser.Header.RG.CN,+                     Data.SAM.Version1_6.Read.Parser.Header.RG.DS,+                     Data.SAM.Version1_6.Read.Parser.Header.RG.DT,+                     Data.SAM.Version1_6.Read.Parser.Header.RG.FO,+                     Data.SAM.Version1_6.Read.Parser.Header.RG.KS,+                     Data.SAM.Version1_6.Read.Parser.Header.RG.LB,+                     Data.SAM.Version1_6.Read.Parser.Header.RG.PG,+                     Data.SAM.Version1_6.Read.Parser.Header.RG.PI,+                     Data.SAM.Version1_6.Read.Parser.Header.RG.PL,+                     Data.SAM.Version1_6.Read.Parser.Header.RG.PM,+                     Data.SAM.Version1_6.Read.Parser.Header.RG.PU,+                     Data.SAM.Version1_6.Read.Parser.Header.RG.SM,+                     Data.SAM.Version1_6.Read.Parser.Header.PG.Base,+                     Data.SAM.Version1_6.Read.Parser.Header.PG.ID,+                     Data.SAM.Version1_6.Read.Parser.Header.PG.PN,+                     Data.SAM.Version1_6.Read.Parser.Header.PG.CL,+                     Data.SAM.Version1_6.Read.Parser.Header.PG.PP,+                     Data.SAM.Version1_6.Read.Parser.Header.PG.DS,+                     Data.SAM.Version1_6.Read.Parser.Header.PG.VN,+                     Data.SAM.Version1_6.Read.Parser.Header.CO.Base++    -- Modules included in this library but not exported.+    -- other-modules:++    -- 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,+                      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 ++    -- Directories containing source files.+    hs-source-dirs:   src++    -- Base language which the package is written in.+    default-language: Haskell2010++test-suite hs-samtools-test+    -- Import common warning flags.+    import:           warnings++    -- Base language which the package is written in.+    default-language: Haskell2010++    -- Modules included in this executable, other than Main.+    -- other-modules:++    -- LANGUAGE extensions used by modules in this package.+    -- other-extensions:++    -- The interface type and version of the test suite.+    type:             exitcode-stdio-1.0++    -- Directories containing source files.+    hs-source-dirs:   test++    -- The entrypoint to the test suite.+    main-is:          Main.hs++    -- Test dependencies.+    build-depends:+        base ^>=4.17.1.0,+        hs-samtools
+ src/Data/SAM/Version1_6/Alignment.hs view
@@ -0,0 +1,46 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Alignment+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Alignment ( -- * SAM version 1.6 alignment mandatory and optional data types (RE-EXPORT)+                                       module Data.SAM.Version1_6.Alignment.Base+                                     ) where++-- | Re-exports.+import Data.SAM.Version1_6.Alignment.Base
+ src/Data/SAM/Version1_6/Alignment/BOPT.hs view
@@ -0,0 +1,278 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Alignment.BOPT+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Alignment.BOPT ( -- * SAM version 1.6 alignment optional fields data type+                                            SAM_V1_6_Alignment_BOPT(..),+                                            SAM_V1_6_Alignment_BOPT_Int8(..),+                                            SAM_V1_6_Alignment_BOPT_Word8(..),+                                            SAM_V1_6_Alignment_BOPT_Int16(..),+                                            SAM_V1_6_Alignment_BOPT_Word16(..),+                                            SAM_V1_6_Alignment_BOPT_Int32(..),+                                            SAM_V1_6_Alignment_BOPT_Word32(..),+                                            SAM_V1_6_Alignment_BOPT_Float(..)+                                          ) where++import Data.Data+import Data.Int+import Data.Sequence+import Data.Word+import Generics.Deriving.Base+++-- | Custom SAM (version 1.6) @"SAM_V1_6_Alignment_BOPT"@ data type.+--+-- See section 1.5 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data SAM_V1_6_Alignment_BOPT = SAM_V1_6_Alignment_BOPT { sam_v1_6_alignment_bopt_int8   :: Maybe SAM_V1_6_Alignment_BOPT_Int8+                                                       , sam_v1_6_alignment_bopt_word8  :: Maybe SAM_V1_6_Alignment_BOPT_Word8+                                                       , sam_v1_6_alignment_bopt_int16  :: Maybe SAM_V1_6_Alignment_BOPT_Int16+                                                       , sam_v1_6_alignment_bopt_word16 :: Maybe SAM_V1_6_Alignment_BOPT_Word16+                                                       , sam_v1_6_alignment_bopt_int32  :: Maybe SAM_V1_6_Alignment_BOPT_Int32+                                                       , sam_v1_6_alignment_bopt_word32 :: Maybe SAM_V1_6_Alignment_BOPT_Word32+                                                       , sam_v1_6_alignment_bopt_float  :: Maybe SAM_V1_6_Alignment_BOPT_Float+                                                       }+  deriving (Generic,Typeable)++instance Show SAM_V1_6_Alignment_BOPT where+  show (SAM_V1_6_Alignment_BOPT int8+                                word8+                                int16+                                word16+                                int32+                                word32+                                float+       ) =+    "SAM_V1_6_Alignment_BOPT { "           +++    "sam_v1_6_alignment_bopt_int8 = "      +++    (show int8)                            +++    " , sam_v1_6_alignment_bopt_word8 = "  +++    (show word8)                           +++    " , sam_v1_6_alignment_bopt_int16 = "  +++    (show int16)                           +++    " , sam_v1_6_alignment_bopt_word16 = " +++    (show word16)                          +++    " , sam_v1_6_alignment_bopt_int32 = "  +++    (show int32)                           +++    " , sam_v1_6_alignment_bopt_word32 = " +++    (show word32)                          +++    " , sam_v1_6_alignment_bopt_float = "  +++    (show float)                           +++    " }"++-- | __c__CsSiIf of the last optional field (type B).+--+-- See section 1.5 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data SAM_V1_6_Alignment_BOPT_Int8 = SAM_V1_6_Alignment_BOPT_Int8 { sam_v1_6_alignment_bopt_int8_tag   :: Seq Word8+                                                                 , sam_v1_6_alignment_bopt_int8_type  :: Word8+                                                                 , sam_v1_6_alignment_bopt_int8_value :: Seq Int8+                                                                 }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Alignment_BOPT_Int8 where+  SAM_V1_6_Alignment_BOPT_Int8 sam_v1_6_alignment_bopt_int8_tag1 sam_v1_6_alignment_bopt_int8_type1 sam_v1_6_alignment_bopt_int8_value1 == SAM_V1_6_Alignment_BOPT_Int8 sam_v1_6_alignment_bopt_int8_tag2 sam_v1_6_alignment_bopt_int8_type2 sam_v1_6_alignment_bopt_int8_value2 = sam_v1_6_alignment_bopt_int8_tag1 == sam_v1_6_alignment_bopt_int8_tag2 && sam_v1_6_alignment_bopt_int8_type1 == sam_v1_6_alignment_bopt_int8_type2 && sam_v1_6_alignment_bopt_int8_value1 == sam_v1_6_alignment_bopt_int8_value2++instance Show SAM_V1_6_Alignment_BOPT_Int8 where+  show (SAM_V1_6_Alignment_BOPT_Int8 tag+                                     bopttype+                                     value+       ) =+    "SAM_V1_6_Alignment_BOPT_Int8 { " +++    "tag  = "                         +++    (show tag)                        +++    " , type = "                      +++    (show bopttype)                   +++    " , value = "                     +++    (show value)                      +++    " }"++-- | c__C__sSiIf of the last optional field (type B).+--+-- See section 1.5 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data SAM_V1_6_Alignment_BOPT_Word8 = SAM_V1_6_Alignment_BOPT_Word8 { sam_v1_6_alignment_bopt_word8_tag   :: Seq Word8+                                                                   , sam_v1_6_alignment_bopt_word8_type  :: Word8+                                                                   , sam_v1_6_alignment_bopt_word8_value :: Seq Word8+                                                                   }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Alignment_BOPT_Word8 where+  SAM_V1_6_Alignment_BOPT_Word8 sam_v1_6_alignment_bopt_word8_tag1 sam_v1_6_alignment_bopt_word8_type1 sam_v1_6_alignment_bopt_word8_value1 == SAM_V1_6_Alignment_BOPT_Word8 sam_v1_6_alignment_bopt_word8_tag2 sam_v1_6_alignment_bopt_word8_type2 sam_v1_6_alignment_bopt_word8_value2 = sam_v1_6_alignment_bopt_word8_tag1 == sam_v1_6_alignment_bopt_word8_tag2 && sam_v1_6_alignment_bopt_word8_type1 == sam_v1_6_alignment_bopt_word8_type2 && sam_v1_6_alignment_bopt_word8_value1 == sam_v1_6_alignment_bopt_word8_value2++instance Show SAM_V1_6_Alignment_BOPT_Word8 where+  show (SAM_V1_6_Alignment_BOPT_Word8 tag+                                      bopttype+                                      value+       ) =+    "SAM_V1_6_Alignment_BOPT_Word8 { " +++    "tag  = "                          +++    (show tag)                         +++    " , type = "                       +++    (show bopttype)                    +++    " , value = "                      +++    (show value)                       +++    " }"++-- | cC__s__SiIf of the last optional field (type B).+--+-- See section 1.5 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data SAM_V1_6_Alignment_BOPT_Int16 = SAM_V1_6_Alignment_BOPT_Int16 { sam_v1_6_alignment_bopt_int16_tag   :: Seq Word8+                                                                   , sam_v1_6_alignment_bopt_int16_type  :: Word8+                                                                   , sam_v1_6_alignment_bopt_int16_value :: Seq Int16+                                                                   }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Alignment_BOPT_Int16 where+  SAM_V1_6_Alignment_BOPT_Int16 sam_v1_6_alignment_bopt_int16_tag1 sam_v1_6_alignment_bopt_int16_type1 sam_v1_6_alignment_bopt_int16_value1 == SAM_V1_6_Alignment_BOPT_Int16 sam_v1_6_alignment_bopt_int16_tag2 sam_v1_6_alignment_bopt_int16_type2 sam_v1_6_alignment_bopt_int16_value2 = sam_v1_6_alignment_bopt_int16_tag1 == sam_v1_6_alignment_bopt_int16_tag2 && sam_v1_6_alignment_bopt_int16_type1 == sam_v1_6_alignment_bopt_int16_type2 && sam_v1_6_alignment_bopt_int16_value1 == sam_v1_6_alignment_bopt_int16_value2++instance Show SAM_V1_6_Alignment_BOPT_Int16 where+  show (SAM_V1_6_Alignment_BOPT_Int16 tag+                                      bopttype+                                      value+       ) =+    "SAM_V1_6_Alignment_BOPT_Int16 { " +++    "tag  = "                          +++    (show tag)                         +++    " , type = "                       +++    (show bopttype)                    +++    " , value = "                      +++    (show value)                       +++    " }"++-- | cCs__S__iIf of the last optional field (type B).+--+-- See section 1.5 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data SAM_V1_6_Alignment_BOPT_Word16 = SAM_V1_6_Alignment_BOPT_Word16 { sam_v1_6_alignment_bopt_word16_tag   :: Seq Word8+                                                                     , sam_v1_6_alignment_bopt_word16_type  :: Word8+                                                                     , sam_v1_6_alignment_bopt_word16_value :: Seq Word16+                                                                     }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Alignment_BOPT_Word16 where+  SAM_V1_6_Alignment_BOPT_Word16 sam_v1_6_alignment_bopt_word16_tag1 sam_v1_6_alignment_bopt_word16_type1 sam_v1_6_alignment_bopt_word16_value1 == SAM_V1_6_Alignment_BOPT_Word16 sam_v1_6_alignment_bopt_word16_tag2 sam_v1_6_alignment_bopt_word16_type2 sam_v1_6_alignment_bopt_word16_value2 = sam_v1_6_alignment_bopt_word16_tag1 == sam_v1_6_alignment_bopt_word16_tag2 && sam_v1_6_alignment_bopt_word16_type1 == sam_v1_6_alignment_bopt_word16_type2 && sam_v1_6_alignment_bopt_word16_value1 == sam_v1_6_alignment_bopt_word16_value2++instance Show SAM_V1_6_Alignment_BOPT_Word16 where+  show (SAM_V1_6_Alignment_BOPT_Word16 tag+                                       bopttype+                                       value+       ) =+    "SAM_V1_6_Alignment_BOPT_Word16 { " +++    "tag  = "                           +++    (show tag)                          +++    " , type = "                        +++    (show bopttype)                     +++    " , value = "                       +++    (show value)                        +++    " }"++-- | cCsS__i__If of the last optional field (type B).+--+-- See section 1.5 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data SAM_V1_6_Alignment_BOPT_Int32 = SAM_V1_6_Alignment_BOPT_Int32 { sam_v1_6_alignment_bopt_int32_tag   :: Seq Word8+                                                                   , sam_v1_6_alignment_bopt_int32_type  :: Word8+                                                                   , sam_v1_6_alignment_bopt_int32_value :: Seq Int32+                                                                   }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Alignment_BOPT_Int32 where+  SAM_V1_6_Alignment_BOPT_Int32 sam_v1_6_alignment_bopt_int32_tag1 sam_v1_6_alignment_bopt_int32_type1 sam_v1_6_alignment_bopt_int32_value1 == SAM_V1_6_Alignment_BOPT_Int32 sam_v1_6_alignment_bopt_int32_tag2 sam_v1_6_alignment_bopt_int32_type2 sam_v1_6_alignment_bopt_int32_value2 = sam_v1_6_alignment_bopt_int32_tag1 == sam_v1_6_alignment_bopt_int32_tag2 && sam_v1_6_alignment_bopt_int32_type1 == sam_v1_6_alignment_bopt_int32_type2 && sam_v1_6_alignment_bopt_int32_value1 == sam_v1_6_alignment_bopt_int32_value2++instance Show SAM_V1_6_Alignment_BOPT_Int32 where+  show (SAM_V1_6_Alignment_BOPT_Int32 tag+                                      bopttype+                                      value+       ) =+    "SAM_V1_6_Alignment_BOPT_Int32 { " +++    "tag  = "                          +++    (show tag)                         +++    " , type = "                       +++    (show bopttype)                    +++    " , value = "                      +++    (show value)                       +++    " }"++-- | cCsSi__I__f of the last optional field (type B).+--+-- See section 1.5 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data SAM_V1_6_Alignment_BOPT_Word32 = SAM_V1_6_Alignment_BOPT_Word32 { sam_v1_6_alignment_bopt_word32_tag   :: Seq Word8+                                                                     , sam_v1_6_alignment_bopt_word32_type  :: Word8+                                                                     , sam_v1_6_alignment_bopt_word32_value :: Seq Word32+                                                                     }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Alignment_BOPT_Word32 where+  SAM_V1_6_Alignment_BOPT_Word32 sam_v1_6_alignment_bopt_word32_tag1 sam_v1_6_alignment_bopt_word32_type1 sam_v1_6_alignment_bopt_word32_value1 == SAM_V1_6_Alignment_BOPT_Word32 sam_v1_6_alignment_bopt_word32_tag2 sam_v1_6_alignment_bopt_word32_type2 sam_v1_6_alignment_bopt_word32_value2 = sam_v1_6_alignment_bopt_word32_tag1 == sam_v1_6_alignment_bopt_word32_tag2 && sam_v1_6_alignment_bopt_word32_type1 == sam_v1_6_alignment_bopt_word32_type2 && sam_v1_6_alignment_bopt_word32_value1 == sam_v1_6_alignment_bopt_word32_value2++instance Show SAM_V1_6_Alignment_BOPT_Word32 where+  show (SAM_V1_6_Alignment_BOPT_Word32 tag+                                       bopttype+                                       value+       ) =+    "SAM_V1_6_Alignment_BOPT_Word32 { " +++    "tag  = "                           +++    (show tag)                          +++    " , type = "                        +++    (show bopttype)                     +++    " , value = "                       +++    (show value)                        +++    " }"++-- | cCsSiI__f__ of the last optional field (type B).+--+-- See section 1.5 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data SAM_V1_6_Alignment_BOPT_Float = SAM_V1_6_Alignment_BOPT_Float { sam_v1_6_alignment_bopt_float_tag   :: Seq Word8+                                                                   , sam_v1_6_alignment_bopt_float_type  :: Word8+                                                                   , sam_v1_6_alignment_bopt_float_value :: Seq Float+                                                                   }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Alignment_BOPT_Float where+  SAM_V1_6_Alignment_BOPT_Float sam_v1_6_alignment_bopt_float_tag1 sam_v1_6_alignment_bopt_float_type1 sam_v1_6_alignment_bopt_float_value1 == SAM_V1_6_Alignment_BOPT_Float sam_v1_6_alignment_bopt_float_tag2 sam_v1_6_alignment_bopt_float_type2 sam_v1_6_alignment_bopt_float_value2 = sam_v1_6_alignment_bopt_float_tag1 == sam_v1_6_alignment_bopt_float_tag2 && sam_v1_6_alignment_bopt_float_type1 == sam_v1_6_alignment_bopt_float_type2 && sam_v1_6_alignment_bopt_float_value1 == sam_v1_6_alignment_bopt_float_value2++instance Show SAM_V1_6_Alignment_BOPT_Float where+  show (SAM_V1_6_Alignment_BOPT_Float tag+                                      bopttype+                                      value+       ) =+    "SAM_V1_6_Alignment_BOPT_Float { " +++    "tag  = "                           +++    (show tag)                          +++    " , type = "                        +++    (show bopttype)                     +++    " , value = "                       +++    (show value)                        +++    " }"
+ src/Data/SAM/Version1_6/Alignment/Base.hs view
@@ -0,0 +1,151 @@+{-# LANGUAGE DeriveDataTypeable          #-}+{-# LANGUAGE DeriveGeneric               #-}+{-# LANGUAGE FlexibleContexts            #-}+{-# LANGUAGE FlexibleInstances           #-}+{-# LANGUAGE MultiParamTypeClasses       #-}+{-# LANGUAGE OverloadedLists             #-}+{-# LANGUAGE OverloadedStrings           #-}+{-# LANGUAGE PackageImports              #-}+{-# LANGUAGE RecordWildCards             #-}+{-# LANGUAGE TemplateHaskell             #-}+{-# LANGUAGE TypeFamilies                #-}+{-# Language QuasiQuotes                 #-}+{-# OPTIONS_GHC -fno-warn-name-shadowing #-}++-- |+-- Module      :  Data.SAM.Version1_6.Alignment.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.SAM.Version1_6.Alignment.Base ( -- * SAM version 1.6 alignment mandatory and optional data types+                                            SAM_V1_6_Alignment(..)+                                          ) where++import Data.SAM.Version1_6.Alignment.BOPT++import Data.ByteString+import Data.Data+import Data.Sequence+import Data.Word+import Generics.Deriving.Base++-- | Custom SAM (version 1.6) @"SAM_V1_6_Alignment"@ data type.+--+-- See section 1.4 and 1.5 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data SAM_V1_6_Alignment = SAM_V1_6_Alignment { sam_v1_6_alignment_qname :: ByteString                    -- ^ Query template NAME.+                                                                                                         -- reads/segments having identical QNAME are regarded to come from+                                                                                                         -- the same template. A QNAME ‘*’ indicates the information+                                                                                                         -- is unavailable. In a SAM file, a read may+                                                                                                         -- occupy multiple alignment lines, when its alignment is chimeric+                                                                                                         -- or when multiple mappings are given.+                                             , sam_v1_6_alignment_flag  :: Int                           -- ^ Combination of bitwise FLAGs.+                                             , sam_v1_6_alignment_rname :: ByteString                    -- ^ Reference sequence NAME of the alignment.+                                                                                                         -- If @SQ header lines are present, RNAME (if not+                                                                                                         -- ‘*’) must be present in one of the SQ-SN tag.+                                                                                                         -- An unmapped segment without coordinate has a ‘*’ at+                                                                                                         -- this field. However, an unmapped segment may also have+                                                                                                         -- an ordinary coordinate such that it can be+                                                                                                         -- placed at a desired position after sorting.+                                                                                                         -- If RNAME is ‘*’, no assumptions can be made about POS+                                                                                                         -- and CIGAR.+                                             , sam_v1_6_alignment_pos   :: Integer                       -- ^ 1-based leftmost mapping POSition of the first CIGAR+                                                                                                         -- operation that “consumes” a reference+                                                                                                         -- base. The first base in a reference sequence has coordinate 1.+                                                                                                         -- POS is set as 0 for an unmapped read without coordinate.+                                                                                                         -- If POS is 0, no assumptions can be made about RNAME and CIGAR.+                                             , sam_v1_6_alignment_mapq  :: Int                           -- ^ MAPping Quality. It equals −10 log10 Pr{mapping position is wrong},+                                                                                                         -- rounded to the nearest integer. A value 255 indicates that the+                                                                                                         -- mapping quality is not available.+                                             , sam_v1_6_alignment_cigar :: ByteString                    -- ^ CIGAR string (set ‘*’ if unavailable).+                                             , sam_v1_6_alignment_rnext :: ByteString                    -- ^ Reference sequence name of the primary alignment of the+                                                                                                         -- NEXT read in the template. For the last read, the next read+                                                                                                         -- is the first read in the template. If @SQ header lines are present,+                                                                                                         -- RNEXT (if not ‘*’ or ‘=’) must be present in one of the SQ-SN tag.+                                                                                                         -- This field is set as ‘*’ when the information is unavailable,+                                                                                                         -- and set as ‘=’ if RNEXT is identical RNAME. If not ‘=’ and the next+                                                                                                         -- read in the template has one primary mapping (see also bit 0x100 in FLAG),+                                                                                                         -- this field is identical to RNAME at the primary line of the next read.+                                                                                                         -- If RNEXT is ‘*’, no assumptions can be made on PNEXT and bit 0x20.+                                             , sam_v1_6_alignment_pnext :: Integer                       -- ^ 1-based Position of the primary alignment of the NEXT read in+                                                                                                         -- the template. Set as 0 when the information is unavailable.+                                                                                                         -- This field equals POS at the primary line of the next read.+                                                                                                         -- If PNEXT is 0, no assumptions can be made on RNEXT and bit 0x20.+                                             , sam_v1_6_alignment_tlen  :: Integer                       -- ^ signed observed Template LENgth. For primary reads where the primary+                                                                                                         -- alignments of all reads in the template are mapped to the same reference+                                                                                                         -- sequence, the absolute value of TLEN equals the distance between the+                                                                                                         -- mapped end of the template and the mapped start of the template,+                                                                                                         -- inclusively (i.e., end − start + 1).+                                                                                                         -- Note that mapped base is defined to be one that aligns to the+                                                                                                         -- reference as described by CIGAR, hence excludes soft-clipped bases.+                                                                                                         -- The TLEN field is positive for the leftmost segment of the template,+                                                                                                         -- negative for the rightmost, and the sign for any middle segment is undefined.+                                                                                                         -- If segments cover the same coordinates then the choice of which is leftmost+                                                                                                         -- and rightmost is arbitrary, but the two ends must still have differing signs.+                                                                                                         -- It is set as 0 for a single-segment template or when the information+                                                                                                         -- is unavailable (e.g., when the first or last segment of a multi-segment+                                                                                                         -- template is unmapped or when the two are mapped to+                                                                                                         -- different reference sequences).+                                             , sam_v1_6_alignment_seq   :: ByteString                    -- ^ segment SEQuence. This field can be a ‘*’ when the sequence+                                                                                                         -- is not stored. If not a ‘*’, the length of the sequence must+                                                                                                         -- equal the sum of lengths of M/I/S/=/X operations in CIGAR.+                                                                                                         -- An ‘=’ denotes the base is identical to the reference base.+                                                                                                         -- No assumptions can be made on the letter cases.+                                             , sam_v1_6_alignment_qual  :: ByteString                    -- ^ ASCII of base QUALity plus 33 (same as the quality string+                                                                                                         -- in the Sanger FASTQ format). A base quality is the phred-scaled+                                                                                                         -- base error probability which equals −10 log10 Pr{base is wrong}.+                                                                                                         -- This field can be a ‘*’ when quality is not stored.+                                                                                                         -- If not a ‘*’, SEQ must not be a ‘*’ and the length of the quality+                                                                                                         -- string ought to equal the length of SEQ.+                                             , sam_v1_6_alignment_aopt  :: Maybe ByteString              -- ^ A - [!-~] - Printable characters.+                                             , sam_v1_6_alignment_iopt  :: Maybe Integer                 -- ^ i - [-+]?[0-9]+ - Signed integer.+                                             , sam_v1_6_alignment_fopt  :: Maybe Float                   -- ^ f - [-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? - Single-precision floating number.+                                             , sam_v1_6_alignment_zopt  :: Maybe ByteString              -- ^ Z - [ !-~]* - Printable string, including space.+                                             , sam_v1_6_alignment_hopt  :: Maybe (Seq Word8)             -- ^ H - ([0-9A-F][0-9A-F])* - Byte array in the Hex format.+                                             , sam_v1_6_alignment_bopt  :: Maybe SAM_V1_6_Alignment_BOPT -- ^ B - [cCsSiIf]&#8203;(,[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* - Integer or numeric array.+                                             }+  deriving (Generic,Typeable)++instance Show SAM_V1_6_Alignment where+  show (SAM_V1_6_Alignment qname flag rname pos mapq cigar rnext pnext tlen seq qual aopt iopt fopt zopt hopt bopt) =+    "SAM_V1_6_Alignment { " +++    "qname = "              +++    (show qname)            +++    " , flag = "            +++    (show flag)             +++    " , rname = "           +++    (show rname)            +++    " , pos = "             +++    (show pos)              +++    " , mapq = "            +++    (show mapq)             +++    " , cigar = "           +++    (show cigar)            +++    " , rnext = "           +++    (show rnext)            +++    " , pnext = "           +++    (show pnext)            +++    " , tlen = "            +++    (show tlen)             +++    " , seq = "             +++    (show seq)              +++    " , qual = "            +++    (show qual)             +++    " , aopt = "            +++    ( show aopt)            +++    " , iopt = "            +++    (show iopt)             +++    " , fopt = "            +++    (show fopt)             +++    " , zopt = "            +++    (show zopt)             +++    " , hopt = "            +++    (show hopt)             +++    " , bopt = "            +++    (show bopt)             +++    " }"
+ src/Data/SAM/Version1_6/Base.hs view
@@ -0,0 +1,80 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.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.SAM.Version1_6.Base ( -- * SAM version 1.6 data type+                                  SAM_V1_6(..)+                                ) where++import Data.SAM.Version1_6.Alignment+import Data.SAM.Version1_6.Header++import Data.Data+import Data.Sequence+import Generics.Deriving.Base++-- | Custom @"SAM_V1_6"@ (SAM version 1.6) data type.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data SAM_V1_6 = SAM_V1_6 { sam_v1_6_file_level_metadata           :: Maybe SAM_V1_6_File_Level_Metadata                 -- ^ File-level metadata.+                                                                                                                        -- Optional. If present,+                                                                                                                        -- there must be only one+                                                                                                                        -- @HD line and it must be+                                                                                                                        -- the first line of the file. +                         , sam_v1_6_reference_sequence_dictionary :: Maybe (Seq SAM_V1_6_Reference_Sequence_Dictionary) -- ^ Reference sequence dictionary.+                                                                                                                        -- The order of @SQ lines defines the+                                                                                                                        -- alignment sorting order.+                         , sam_v1_6_read_group                    :: Maybe (Seq SAM_V1_6_Read_Group)                    -- ^ Read group.+                                                                                                                        -- Unordered multiple @RG+                                                                                                                        -- lines are allowed.+                         , sam_v1_6_program                       :: Maybe SAM_V1_6_Program                             -- ^ Program.+                         , sam_v1_6_one_line_comment              :: Maybe (Seq SAM_V1_6_One_Line_Comment)              -- ^ One-line text comment.+                                                                                                                        -- Unordered multiple @CO lines+                                                                                                                        -- are allowed. UTF-8 encoding+                                                                                                                        -- may be used.+                         , sam_v1_6_alignment                     :: Seq SAM_V1_6_Alignment                             -- ^ The alignment section (mandatory+                                                                                                                        -- and optional fields).+                         }+  deriving (Generic,Typeable)++instance Show SAM_V1_6 where+  show (SAM_V1_6 file_level_metadata+                 reference_sequence_dictionary+                 read_group program+                 one_line_comment+                 alignment+       ) =+    "SAM_V1_6 { "                         +++    "file_level_metadata = "              +++    (show file_level_metadata)            +++    " , reference_sequence_dictionary = " +++    (show reference_sequence_dictionary)  +++    " , read_group = "                    +++    (show read_group)                     +++    " , program = "                       +++    (show program)                        +++    " , one_line_comment = "              +++    (show one_line_comment)               +++    " , alignment = "                     +++    (show alignment)                      +++    " }"
+ src/Data/SAM/Version1_6/Header.hs view
@@ -0,0 +1,54 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Header+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Header ( -- * SAM version 1.6 header section data type (RE-EXPORT)+                                    module Data.SAM.Version1_6.Header.CO,+                                    module Data.SAM.Version1_6.Header.HD,+                                    module Data.SAM.Version1_6.Header.PG,+                                    module Data.SAM.Version1_6.Header.RG,+                                    module Data.SAM.Version1_6.Header.SQ+                                  ) where++-- | Re-exports.+import Data.SAM.Version1_6.Header.CO+import Data.SAM.Version1_6.Header.HD+import Data.SAM.Version1_6.Header.PG+import Data.SAM.Version1_6.Header.RG+import Data.SAM.Version1_6.Header.SQ
+ src/Data/SAM/Version1_6/Header/CO.hs view
@@ -0,0 +1,47 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Header.CO+-- 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.SAM.Version1_6.Header.CO ( -- * SAM version 1.6 One-line text comment data type+                                       SAM_V1_6_One_Line_Comment(..)+                                     ) where++import Data.ByteString+import Data.Data+import Generics.Deriving.Base++-- | Custom SAM (version 1.6) @"SAM_V1_6_One_Line_Comment"@ data type.+--+-- See section 1.3 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data SAM_V1_6_One_Line_Comment = SAM_V1_6_One_Line_Comment { sam_v1_6_one_line_comment_value :: ByteString+                                                           }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_One_Line_Comment where+  SAM_V1_6_One_Line_Comment sam_v1_6_one_line_comment_value1 == SAM_V1_6_One_Line_Comment sam_v1_6_one_line_comment_value2 = sam_v1_6_one_line_comment_value1 == sam_v1_6_one_line_comment_value2++instance Show SAM_V1_6_One_Line_Comment where+  show (SAM_V1_6_One_Line_Comment value) = "SAM_V1_6_One_Line_Comment { " +++                                               "value = "                     +++                                               (show value)                   +++                                               " }"
+ src/Data/SAM/Version1_6/Header/HD.hs view
@@ -0,0 +1,133 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Header.HD+-- 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.SAM.Version1_6.Header.HD ( -- * SAM version 1.6 File-level metadata data type+                                       SAM_V1_6_File_Level_Metadata(..),+                                       -- * SAM version 1.6 File-Level Metadata data types+                                       SAM_V1_6_File_Level_Metadata_Format_Version(..),+                                       SAM_V1_6_File_Level_Metadata_Sorting_Order(..),+                                       SAM_V1_6_File_Level_Metadata_Alignment_Grouping(..),+                                       SAM_V1_6_File_Level_Metadata_SubSorting_Order(..)+                                     ) where++import Data.ByteString+import Data.Data+import Data.Sequence+import Data.Word+import Generics.Deriving.Base++-- | Custom SAM (version 1.6) @"SAM_V1_6_File_Level_Metadata"@ data type.+--+-- See section 1.3 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data SAM_V1_6_File_Level_Metadata = SAM_V1_6_File_Level_Metadata { sam_v1_6_file_level_metadata_format_version     :: SAM_V1_6_File_Level_Metadata_Format_Version+                                                                 , sam_v1_6_file_level_metadata_sorting_order      :: Maybe SAM_V1_6_File_Level_Metadata_Sorting_Order+                                                                 , sam_v1_6_file_level_metadata_alignment_grouping :: Maybe SAM_V1_6_File_Level_Metadata_Alignment_Grouping+                                                                 , sam_v1_6_file_level_metadata_subsorting_order   :: Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order+                                                                 }+   deriving (Generic,Typeable)++instance Show SAM_V1_6_File_Level_Metadata where+  show (SAM_V1_6_File_Level_Metadata version sorting_order alignment_grouping subsorting_order) =+    "SAM_V1_6_File_Level_Metadata { " +++    "version = "                      +++    (show version)                    +++    " , sorting_order = "             +++    (show sorting_order)              +++    " , alignment_grouping = "        +++    (show alignment_grouping)         +++    " , subsorting_order = "          +++    (show subsorting_order)           +++    " }" ++-- | VN tag for @"SAM_V1_6_File_Level_Metadata"@.+data SAM_V1_6_File_Level_Metadata_Format_Version = SAM_V1_6_File_Level_Metadata_Format_Version { sam_v1_6_file_level_metadata_format_version_tag   :: Seq Word8+                                                                                               , sam_v1_6_file_level_metadata_format_version_value :: ByteString+                                                                                               }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_File_Level_Metadata_Format_Version where+  SAM_V1_6_File_Level_Metadata_Format_Version sam_v1_6_file_level_metadata_format_version_tag1 sam_v1_6_file_level_metadata_format_version_value1 == SAM_V1_6_File_Level_Metadata_Format_Version sam_v1_6_file_level_metadata_format_version_tag2 sam_v1_6_file_level_metadata_format_version_value2 = sam_v1_6_file_level_metadata_format_version_tag1 == sam_v1_6_file_level_metadata_format_version_tag2 && sam_v1_6_file_level_metadata_format_version_value1 == sam_v1_6_file_level_metadata_format_version_value2++instance Show SAM_V1_6_File_Level_Metadata_Format_Version where+  show (SAM_V1_6_File_Level_Metadata_Format_Version tag value) =+    "SAM_V1_6_File_Level_Metadata_Format_Version { " +++    "tag = "                                         +++    (show tag)                                       +++    " , value = "                                    +++    (show value)                                     +++    " }"++-- | SO tag for @"SAM_V1_6_File_Level_Metadata"@.+data SAM_V1_6_File_Level_Metadata_Sorting_Order = SAM_V1_6_File_Level_Metadata_Sorting_Order { sam_v1_6_file_level_metadata_sorting_order_tag   :: Seq Word8+                                                                                             , sam_v1_6_file_level_metadata_sorting_order_value :: ByteString+                                                                                             }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_File_Level_Metadata_Sorting_Order where+  SAM_V1_6_File_Level_Metadata_Sorting_Order sam_v1_6_file_level_metadata_sorting_order_tag1 sam_v1_6_file_level_metadata_sorting_order_value1 == SAM_V1_6_File_Level_Metadata_Sorting_Order sam_v1_6_file_level_metadata_sorting_order_tag2 sam_v1_6_file_level_metadata_sorting_order_value2 = sam_v1_6_file_level_metadata_sorting_order_tag1 == sam_v1_6_file_level_metadata_sorting_order_tag2 && sam_v1_6_file_level_metadata_sorting_order_value1 == sam_v1_6_file_level_metadata_sorting_order_value2++instance Show SAM_V1_6_File_Level_Metadata_Sorting_Order where+  show (SAM_V1_6_File_Level_Metadata_Sorting_Order tag value) =+    "SAM_V1_6_File_Level_Metadata_Sorting_Order { " +++    "tag = "                                        +++    (show tag)                                      +++    " , value = "                                   +++    (show value)                                    +++    " }"++-- | GO tag for @"SAM_V1_6_File_Level_Metadata"@.+data SAM_V1_6_File_Level_Metadata_Alignment_Grouping = SAM_V1_6_File_Level_Metadata_Alignment_Grouping { sam_v1_6_file_level_metadata_alignment_grouping_tag   :: Seq Word8+                                                                                                       , sam_v1_6_file_level_metadata_alignment_grouping_value :: ByteString+                                                                                                       }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_File_Level_Metadata_Alignment_Grouping where+  SAM_V1_6_File_Level_Metadata_Alignment_Grouping sam_v1_6_file_level_metadata_alignment_grouping_tag1 sam_v1_6_file_level_metadata_alignment_grouping_value1 == SAM_V1_6_File_Level_Metadata_Alignment_Grouping sam_v1_6_file_level_metadata_alignment_grouping_tag2 sam_v1_6_file_level_metadata_alignment_grouping_value2 = sam_v1_6_file_level_metadata_alignment_grouping_tag1 == sam_v1_6_file_level_metadata_alignment_grouping_tag2 && sam_v1_6_file_level_metadata_alignment_grouping_value1 == sam_v1_6_file_level_metadata_alignment_grouping_value2++instance Show SAM_V1_6_File_Level_Metadata_Alignment_Grouping where+  show (SAM_V1_6_File_Level_Metadata_Alignment_Grouping tag value) =+    "SAM_V1_6_File_Level_Metadata_Alignment_Grouping { " +++    "tag = "                                             +++    (show tag)                                           +++    " , value = "                                        +++    (show value)                                         +++    " }"++-- | SS tag for @"SAM_V1_6_File_Level_Metadata"@.+data SAM_V1_6_File_Level_Metadata_SubSorting_Order = SAM_V1_6_File_Level_Metadata_SubSorting_Order { sam_v1_6_file_level_metadata_subsorting_order_tag   :: Seq Word8+                                                                                                   , sam_v1_6_file_level_metadata_subsorting_order_value :: ByteString+                                                                                                   }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_File_Level_Metadata_SubSorting_Order where+  SAM_V1_6_File_Level_Metadata_SubSorting_Order sam_v1_6_file_level_metadata_subsorting_order_tag1 sam_v1_6_file_level_metadata_subsorting_order_value1 == SAM_V1_6_File_Level_Metadata_SubSorting_Order sam_v1_6_file_level_metadata_subsorting_order_tag2 sam_v1_6_file_level_metadata_subsorting_order_value2 = sam_v1_6_file_level_metadata_subsorting_order_tag1 == sam_v1_6_file_level_metadata_subsorting_order_tag2 && sam_v1_6_file_level_metadata_subsorting_order_value1 == sam_v1_6_file_level_metadata_subsorting_order_value2++instance Show SAM_V1_6_File_Level_Metadata_SubSorting_Order where+  show (SAM_V1_6_File_Level_Metadata_SubSorting_Order tag value) =+    "SAM_V1_6_File_Level_Metadata_SubSorting_Order { " +++    "tag = "                                           +++    (show tag)                                         +++    " , value = "                                      +++    (show value)                                       +++    " }"
+ src/Data/SAM/Version1_6/Header/PG.hs view
@@ -0,0 +1,177 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Header.PG+-- 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.SAM.Version1_6.Header.PG ( -- * SAM version 1.6 program data type+                                       SAM_V1_6_Program(..),+                                       -- * SAM version 1.6 program data types+                                       SAM_V1_6_Program_Record_Identifier(..),+                                       SAM_V1_6_Program_Name(..),+                                       SAM_V1_6_Program_Command_Line(..),+                                       SAM_V1_6_Program_Previous_PG_ID(..),+                                       SAM_V1_6_Program_Description(..),+                                       SAM_V1_6_Program_Version(..)+                                     ) where++import Data.ByteString+import Data.Data+import Data.Sequence+import Data.Word+import Generics.Deriving.Base++-- | Custom SAM (version 1.6) @"SAM_V1_6_Program"@ data type.+--+-- See section 1.3 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data SAM_V1_6_Program = SAM_V1_6_Program { sam_v1_6_program_record_identifier :: SAM_V1_6_Program_Record_Identifier+                                         , sam_v1_6_program_name              :: Maybe SAM_V1_6_Program_Name+                                         , sam_v1_6_program_command_line      :: Maybe SAM_V1_6_Program_Command_Line+                                         , sam_v1_6_program_previous_pg_id    :: Maybe SAM_V1_6_Program_Previous_PG_ID+                                         , sam_v1_6_program_description       :: Maybe SAM_V1_6_Program_Description+                                         , sam_v1_6_program_version           :: Maybe SAM_V1_6_Program_Version+                                         }+  deriving (Generic,Typeable)++instance Show SAM_V1_6_Program where+  show (SAM_V1_6_Program record_identifier name command_line previous_pg_id description version) =+    "SAM_V1_6_Program { "    +++    "record_identifier = "   +++    (show record_identifier) +++    " , name = "             +++    (show name)              +++    " , command_line = "     +++    (show command_line)      +++    " , previous_pg_id = "   +++    (show previous_pg_id)    +++    " , description = "      +++    (show description)       +++    " , version = "          +++    (show version)           +++    " }"++-- | ID tag for @"SAM_V1_6_Program"@.+data SAM_V1_6_Program_Record_Identifier = SAM_V1_6_Program_Record_Identifier { sam_v1_6_program_record_identifier_tag   :: Seq Word8+                                                                             , sam_v1_6_program_record_identifier_value :: ByteString+                                                                             }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Program_Record_Identifier where+  SAM_V1_6_Program_Record_Identifier sam_v1_6_program_record_identifier_tag1 sam_v1_6_program_record_identifier_value1 == SAM_V1_6_Program_Record_Identifier sam_v1_6_program_record_identifier_tag2 sam_v1_6_program_record_identifier_value2 = sam_v1_6_program_record_identifier_tag1 == sam_v1_6_program_record_identifier_tag2 && sam_v1_6_program_record_identifier_value1 == sam_v1_6_program_record_identifier_value2++instance Show SAM_V1_6_Program_Record_Identifier where+  show (SAM_V1_6_Program_Record_Identifier tag value) =+    "SAM_V1_6_Program_Record_Identifier { " +++    "tag = "                                +++    (show tag)                              +++    " , value = "                           +++    (show value)                            +++    " }"++-- | PN tag for @"SAM_V1_6_Program"@.+data SAM_V1_6_Program_Name = SAM_V1_6_Program_Name { sam_v1_6_program_name_tag   :: Seq Word8+                                                   , sam_v1_6_program_name_value :: ByteString+                                                   }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Program_Name where+  SAM_V1_6_Program_Name sam_v1_6_program_name_tag1 sam_v1_6_program_name_value1 == SAM_V1_6_Program_Name sam_v1_6_program_name_tag2 sam_v1_6_program_name_value2 = sam_v1_6_program_name_tag1 == sam_v1_6_program_name_tag2 && sam_v1_6_program_name_value1 == sam_v1_6_program_name_value2++instance Show SAM_V1_6_Program_Name where+  show (SAM_V1_6_Program_Name tag value) =+    "SAM_V1_6_Program_Name { " +++    "tag = "                   +++    (show tag)                 +++    " , value = "              +++    (show value)               +++    " }"++-- | CL tag for @"SAM_V1_6_Program"@.+data SAM_V1_6_Program_Command_Line = SAM_V1_6_Program_Command_Line { sam_v1_6_program_command_line_tag   :: Seq Word8+                                                                   , sam_v1_6_program_command_line_value :: ByteString+                                                                   }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Program_Command_Line where+  SAM_V1_6_Program_Command_Line sam_v1_6_program_command_line_tag1 sam_v1_6_program_command_line_value1 == SAM_V1_6_Program_Command_Line sam_v1_6_program_command_line_tag2 sam_v1_6_program_command_line_value2 = sam_v1_6_program_command_line_tag1 == sam_v1_6_program_command_line_tag2 && sam_v1_6_program_command_line_value1 == sam_v1_6_program_command_line_value2++instance Show SAM_V1_6_Program_Command_Line where+  show (SAM_V1_6_Program_Command_Line tag value) =+    "SAM_V1_6_Program_Command_Line { " +++    "tag = "                           +++    (show tag)                         +++    " , value = "                      +++    (show value)                       +++    " }"++-- | PP tag for @"SAM_V1_6_Program"@.+data SAM_V1_6_Program_Previous_PG_ID = SAM_V1_6_Program_Previous_PG_ID { sam_v1_6_program_previous_pg_id_tag   :: Seq Word8+                                                                       , sam_v1_6_program_previous_pg_id_value :: ByteString+                                                                       }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Program_Previous_PG_ID where+  SAM_V1_6_Program_Previous_PG_ID sam_v1_6_program_previous_pg_id_tag1 sam_v1_6_program_previous_pg_id_value1 == SAM_V1_6_Program_Previous_PG_ID sam_v1_6_program_previous_pg_id_tag2 sam_v1_6_program_previous_pg_id_value2 = sam_v1_6_program_previous_pg_id_tag1 == sam_v1_6_program_previous_pg_id_tag2 && sam_v1_6_program_previous_pg_id_value1 == sam_v1_6_program_previous_pg_id_value2++instance Show SAM_V1_6_Program_Previous_PG_ID where+  show (SAM_V1_6_Program_Previous_PG_ID tag value) =+    "SAM_V1_6_Program_Previous_PG_ID { " +++    "tag = "                             +++    (show tag)                           +++    " , value = "                        +++    (show value)                         +++    " }"++-- | DS tag for @"SAM_V1_6_Program"@.+data SAM_V1_6_Program_Description = SAM_V1_6_Program_Description { sam_v1_6_program_description_tag   :: Seq Word8+                                                                 , sam_v1_6_program_description_value :: ByteString+                                                                 }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Program_Description where+  SAM_V1_6_Program_Description sam_v1_6_program_description_tag1 sam_v1_6_program_description_value1 == SAM_V1_6_Program_Description sam_v1_6_program_description_tag2 sam_v1_6_program_description_value2 = sam_v1_6_program_description_tag1 == sam_v1_6_program_description_tag2 && sam_v1_6_program_description_value1 == sam_v1_6_program_description_value2++instance Show SAM_V1_6_Program_Description where+  show (SAM_V1_6_Program_Description tag value) =+    "SAM_V1_6_Program_Description { " +++    "tag = "                          +++    (show tag)                        +++    " , value = "                     +++    (show value)                      +++    " }"++-- | VN tag for @"SAM_V1_6_Program"@.+data SAM_V1_6_Program_Version = SAM_V1_6_Program_Version { sam_v1_6_program_version_tag   :: Seq Word8+                                                         , sam_v1_6_program_version_value :: ByteString+                                                         }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Program_Version where+  SAM_V1_6_Program_Version sam_v1_6_program_version_tag1 sam_v1_6_program_version_value1 == SAM_V1_6_Program_Version sam_v1_6_program_version_tag2 sam_v1_6_program_version_value2 = sam_v1_6_program_version_tag1 == sam_v1_6_program_version_tag2 && sam_v1_6_program_version_value1 == sam_v1_6_program_version_value2++instance Show SAM_V1_6_Program_Version where+  show (SAM_V1_6_Program_Version tag value) =+    "SAM_V1_6_Program_Version { " +++    "tag = "                      +++    (show tag)                    +++    " , value = "                 +++    (show value)                  +++    " }"
+ src/Data/SAM/Version1_6/Header/RG.hs view
@@ -0,0 +1,366 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Header.RG+-- 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.SAM.Version1_6.Header.RG ( -- * SAM version 1.6 Read group data type+                                       SAM_V1_6_Read_Group(..),+                                       -- * SAM version 1.6 Read group data types+                                       SAM_V1_6_Read_Group_Identifier(..),+                                       SAM_V1_6_Read_Group_Barcode_Sequence(..),+                                       SAM_V1_6_Read_Group_Sequencing_Center(..),+                                       SAM_V1_6_Read_Group_Description(..),+                                       SAM_V1_6_Read_Group_Run_Date(..),+                                       SAM_V1_6_Read_Group_Flow_Order(..),+                                       SAM_V1_6_Read_Group_Key_Sequence(..),+                                       SAM_V1_6_Read_Group_Library(..),+                                       SAM_V1_6_Read_Group_Programs(..),+                                       SAM_V1_6_Read_Group_Predicted_Median_Insert_Size(..),+                                       SAM_V1_6_Read_Group_Platform(..),+                                       SAM_V1_6_Read_Group_Platform_Model(..),+                                       SAM_V1_6_Read_Group_Platform_Unit(..),+                                       SAM_V1_6_Read_Group_Sample(..)+                                     ) where++import Data.ByteString+import Data.Data+import Data.Sequence+import Data.Word+import Generics.Deriving.Base++-- | Custom SAM (version 1.6) @"SAM_V1_6_Read_Group"@ data type.+--+-- See section 1.3 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data SAM_V1_6_Read_Group = SAM_V1_6_Read_Group { sam_v1_6_read_group_identifer                    :: SAM_V1_6_Read_Group_Identifier+                                               , sam_v1_6_read_group_barcode_sequence             :: Maybe SAM_V1_6_Read_Group_Barcode_Sequence+                                               , sam_v1_6_read_group_sequencing_center            :: Maybe SAM_V1_6_Read_Group_Sequencing_Center+                                               , sam_v1_6_read_group_description                  :: Maybe SAM_V1_6_Read_Group_Description+                                               , sam_v1_6_read_group_run_date                     :: Maybe SAM_V1_6_Read_Group_Run_Date+                                               , sam_v1_6_read_group_flow_order                   :: Maybe SAM_V1_6_Read_Group_Flow_Order+                                               , sam_v1_6_read_group_key_sequence                 :: Maybe SAM_V1_6_Read_Group_Key_Sequence+                                               , sam_v1_6_read_group_library                      :: Maybe SAM_V1_6_Read_Group_Library+                                               , sam_v1_6_read_group_programs                     :: Maybe SAM_V1_6_Read_Group_Programs+                                               , sam_v1_6_read_group_predicted_median_insert_size :: Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size+                                               , sam_v1_6_read_group_platform                     :: Maybe SAM_V1_6_Read_Group_Platform+                                               , sam_v1_6_read_group_platform_model               :: Maybe SAM_V1_6_Read_Group_Platform_Model+                                               , sam_v1_6_read_group_platform_unit                :: Maybe SAM_V1_6_Read_Group_Platform_Unit+                                               , sam_v1_6_read_group_sample                       :: Maybe SAM_V1_6_Read_Group_Sample+                                               }++instance Show SAM_V1_6_Read_Group where+  show (SAM_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+       ) =+    "SAM_V1_6_Read_Group { "                  +++    "read_group_identifier = "                +++    (show group_identifier)                   +++    " , barcode_sequence = "                  +++    (show barcode_sequence)                   +++    " , sequencing_center = "                 +++    (show sequencing_center)                  +++    " , description = "                       +++    (show description)                        +++    " , run_date = "                          +++    (show run_date)                           +++    " , flow_order = "                        +++    (show flow_order)                         +++    " , key_sequence = "                      +++    (show key_sequence)                       +++    " , library = "                           +++    (show library)                            +++    " , programs = "                          +++    (show programs)                           +++    " , show_predicted_median_insert_size = " +++    (show predicted_median_insert_size)       +++    " , platform = "                          +++    (show platform)                           +++    " , platform_model = "                    +++    (show platform_model)                     +++    " , platform_unit = "                     +++    (show platform_unit)                      +++    " , sample = "                            +++    (show sample)                             +++    " }"++-- | ID tag for @"SAM_V1_6_Read_Group"@.+data SAM_V1_6_Read_Group_Identifier = SAM_V1_6_Read_Group_Identifier { sam_v1_6_read_group_identifier_tag   :: Seq Word8+                                                                     , sam_v1_6_read_group_identifier_value :: ByteString+                                                                     }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Read_Group_Identifier where+  SAM_V1_6_Read_Group_Identifier sam_v1_6_read_group_identifier_tag1 sam_v1_6_read_group_identifier_value1 == SAM_V1_6_Read_Group_Identifier sam_v1_6_read_group_identifier_tag2 sam_v1_6_read_group_identifier_value2 = sam_v1_6_read_group_identifier_tag1 == sam_v1_6_read_group_identifier_tag2 && sam_v1_6_read_group_identifier_value1 == sam_v1_6_read_group_identifier_value2++instance Show SAM_V1_6_Read_Group_Identifier where+  show (SAM_V1_6_Read_Group_Identifier tag value) =+    "SAM_V1_6_Read_Group_Identifier { " +++    "tag = "                            +++    (show tag)                          +++    " , value = "                       +++    (show value)                        +++    " }"++-- | BC tag for @"SAM_V1_6_Read_Group"@.+data SAM_V1_6_Read_Group_Barcode_Sequence = SAM_V1_6_Read_Group_Barcode_Sequence { sam_v1_6_read_group_barcode_sequence_tag   :: Seq Word8+                                                                                 , sam_v1_6_read_group_barcode_sequence_value :: ByteString+                                                                                 }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Read_Group_Barcode_Sequence where+  SAM_V1_6_Read_Group_Barcode_Sequence sam_v1_6_read_group_barcode_sequence_tag1 sam_v1_6_read_group_barcode_sequence_value1 == SAM_V1_6_Read_Group_Barcode_Sequence sam_v1_6_read_group_barcode_sequence_tag2 sam_v1_6_read_group_barcode_sequence_value2 = sam_v1_6_read_group_barcode_sequence_tag1 == sam_v1_6_read_group_barcode_sequence_tag2 && sam_v1_6_read_group_barcode_sequence_value1 == sam_v1_6_read_group_barcode_sequence_value2++instance Show SAM_V1_6_Read_Group_Barcode_Sequence where+  show (SAM_V1_6_Read_Group_Barcode_Sequence tag value) =+    "SAM_V1_6_Read_Group_Barcode_Sequence { " +++    "tag = "                                  +++    (show tag)                                +++    " , value = "                             +++    (show value)                              +++    " }"++-- | CN tag for @"SAM_V1_6_Read_Group"@.+data SAM_V1_6_Read_Group_Sequencing_Center = SAM_V1_6_Read_Group_Sequencing_Center { sam_v1_6_read_group_sequencing_center_tag   :: Seq Word8+                                                                                   , sam_v1_6_read_group_sequencing_center_value :: ByteString+                                                                                   }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Read_Group_Sequencing_Center where+  SAM_V1_6_Read_Group_Sequencing_Center sam_v1_6_read_group_sequencing_center_tag1 sam_v1_6_read_group_sequencing_center_value1 == SAM_V1_6_Read_Group_Sequencing_Center sam_v1_6_read_group_sequencing_center_tag2 sam_v1_6_read_group_sequencing_center_value2 = sam_v1_6_read_group_sequencing_center_tag1 == sam_v1_6_read_group_sequencing_center_tag2 && sam_v1_6_read_group_sequencing_center_value1 == sam_v1_6_read_group_sequencing_center_value2++instance Show SAM_V1_6_Read_Group_Sequencing_Center where+  show (SAM_V1_6_Read_Group_Sequencing_Center tag value) =+    "SAM_V1_6_Read_Group_Sequencing_Center { " +++    "tag = "                                   +++    (show tag)                                 +++    " , value = "                              +++    (show value)                               +++    " }"++-- | DS tag for @"SAM_V1_6_Read_Group"@.+data SAM_V1_6_Read_Group_Description = SAM_V1_6_Read_Group_Description { sam_v1_6_read_group_description_tag   :: Seq Word8+                                                                       , sam_v1_6_read_group_description_value :: ByteString+                                                                       }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Read_Group_Description where+  SAM_V1_6_Read_Group_Description sam_v1_6_read_group_description_tag1 sam_v1_6_read_group_description_value1 == SAM_V1_6_Read_Group_Description sam_v1_6_read_group_description_tag2 sam_v1_6_read_group_description_value2 = sam_v1_6_read_group_description_tag1 == sam_v1_6_read_group_description_tag2 && sam_v1_6_read_group_description_value1 == sam_v1_6_read_group_description_value2++instance Show SAM_V1_6_Read_Group_Description where+  show (SAM_V1_6_Read_Group_Description tag value) =+    "SAM_V1_6_Read_Group_Description { " +++    "tag = "                             +++    (show tag)                           +++    " , value = "                        +++    (show value)                         +++    " }"++-- | DT tag for @"SAM_V1_6_Read_Group"@.+data SAM_V1_6_Read_Group_Run_Date = SAM_V1_6_Read_Group_Run_Date { sam_v1_6_read_group_run_date_tag   :: Seq Word8+                                                                 , sam_v1_6_read_group_run_date_value :: ByteString+                                                                 }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Read_Group_Run_Date where+  SAM_V1_6_Read_Group_Run_Date sam_v1_6_read_group_run_date_tag1 sam_v1_6_read_group_run_date_value1 == SAM_V1_6_Read_Group_Run_Date sam_v1_6_read_group_run_date_tag2 sam_v1_6_read_group_run_date_value2 = sam_v1_6_read_group_run_date_tag1 == sam_v1_6_read_group_run_date_tag2 && sam_v1_6_read_group_run_date_value1 == sam_v1_6_read_group_run_date_value2++instance Show SAM_V1_6_Read_Group_Run_Date where+  show (SAM_V1_6_Read_Group_Run_Date tag value) =+    "SAM_V1_6_Read_Group_Run_Date { " +++    "tag = "                          +++    (show tag)                        +++    " , value = "                     +++    (show value)                      +++    " }"++-- | FO tag for @"SAM_V1_6_Read_Group"@.+data SAM_V1_6_Read_Group_Flow_Order = SAM_V1_6_Read_Group_Flow_Order { sam_v1_6_read_group_flow_order_tag :: Seq Word8+                                                                     , sam_v1_6_read_group_flow_order_value :: ByteString+                                                                     }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Read_Group_Flow_Order where+  SAM_V1_6_Read_Group_Flow_Order sam_v1_6_read_group_flow_order_tag1 sam_v1_6_one_line_comment_value1 == SAM_V1_6_Read_Group_Flow_Order sam_v1_6_read_group_flow_order_tag2 sam_v1_6_read_group_flow_order_value2 = sam_v1_6_read_group_flow_order_tag1 == sam_v1_6_read_group_flow_order_tag2 && sam_v1_6_one_line_comment_value1 == sam_v1_6_read_group_flow_order_value2++instance Show SAM_V1_6_Read_Group_Flow_Order where+  show (SAM_V1_6_Read_Group_Flow_Order tag value) =+    "SAM_V1_6_Read_Group_Flow_Order { " +++    "tag = "                            +++    (show tag)                          +++    " , value = "                       +++    (show value)                        +++    " }"++-- | KS tag for @"SAM_V1_6_Read_Group"@.+data SAM_V1_6_Read_Group_Key_Sequence = SAM_V1_6_Read_Group_Key_Sequence { sam_v1_6_read_group_key_sequence_tag   :: Seq Word8+                                                                         , sam_v1_6_read_group_key_sequence_value :: ByteString+                                                                         }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Read_Group_Key_Sequence where+  SAM_V1_6_Read_Group_Key_Sequence sam_v1_6_read_group_key_sequence_tag1 sam_v1_6_read_group_key_sequence_value1 == SAM_V1_6_Read_Group_Key_Sequence sam_v1_6_read_group_key_sequence_tag2 sam_v1_6_read_group_key_sequence_value2 = sam_v1_6_read_group_key_sequence_tag1 == sam_v1_6_read_group_key_sequence_tag2 && sam_v1_6_read_group_key_sequence_value1 == sam_v1_6_read_group_key_sequence_value2++instance Show SAM_V1_6_Read_Group_Key_Sequence where+  show (SAM_V1_6_Read_Group_Key_Sequence tag value) =+    "SAM_V1_6_Read_Group_Key_Sequence { " +++    "tag = "                              +++    (show tag)                            +++    " , value = "                         +++    (show value)                          +++    " }"++-- | LB tag for @"SAM_V1_6_Read_Group"@.+data SAM_V1_6_Read_Group_Library = SAM_V1_6_Read_Group_Library { sam_v1_6_read_group_library_tag   :: Seq Word8+                                                               , sam_v1_6_read_group_library_value :: ByteString+                                                               }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Read_Group_Library where+  SAM_V1_6_Read_Group_Library sam_v1_6_read_group_library_tag1 sam_v1_6_read_group_library_value1 == SAM_V1_6_Read_Group_Library sam_v1_6_read_group_library_tag2 sam_v1_6_read_group_library_value2 = sam_v1_6_read_group_library_tag1 == sam_v1_6_read_group_library_tag2 && sam_v1_6_read_group_library_value1 == sam_v1_6_read_group_library_value2++instance Show SAM_V1_6_Read_Group_Library where+  show (SAM_V1_6_Read_Group_Library tag value) =+    "SAM_V1_6_Read_Group_Library { " +++    "tag = "                         +++    (show tag)                       +++    " , value = "                    +++    (show value)                     +++    " }"++-- | PG tag for @"SAM_V1_6_Read_Group"@.+data SAM_V1_6_Read_Group_Programs = SAM_V1_6_Read_Group_Programs { sam_v1_6_read_group_programs_tag   :: Seq Word8+                                                                 , sam_v1_6_read_group_programs_value :: ByteString+                                                                 }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Read_Group_Programs where+  SAM_V1_6_Read_Group_Programs sam_v1_6_read_group_programs_tag1 sam_v1_6_read_group_programs_value1 == SAM_V1_6_Read_Group_Programs sam_v1_6_read_group_programs_tag2 sam_v1_6_read_group_programs_value2 = sam_v1_6_read_group_programs_tag1 == sam_v1_6_read_group_programs_tag2 && sam_v1_6_read_group_programs_value1 == sam_v1_6_read_group_programs_value2++instance Show SAM_V1_6_Read_Group_Programs where+  show (SAM_V1_6_Read_Group_Programs tag value) =+    "SAM_V1_6_Read_Group_Programs { " +++    "tag = "                          +++    (show tag)                        +++    " , value = "                     +++    (show value)                      +++    " }"++-- | PI tag for @"SAM_V1_6_Read_Group"@.+data SAM_V1_6_Read_Group_Predicted_Median_Insert_Size = SAM_V1_6_Read_Group_Predicted_Median_Insert_Size { sam_v1_6_read_group_predicted_median_insert_size_tag   :: Seq Word8+                                                                                                         , sam_v1_6_read_group_predicted_median_insert_size_value :: ByteString+                                                                                                         }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Read_Group_Predicted_Median_Insert_Size where+  SAM_V1_6_Read_Group_Predicted_Median_Insert_Size sam_v1_6_read_group_predicted_median_insert_size_tag1 sam_v1_6_one_line_comment_value1 == SAM_V1_6_Read_Group_Predicted_Median_Insert_Size sam_v1_6_read_group_predicted_median_insert_size_tag2 sam_v1_6_read_group_predicted_median_insert_size_value2 = sam_v1_6_read_group_predicted_median_insert_size_tag1 == sam_v1_6_read_group_predicted_median_insert_size_tag2 && sam_v1_6_one_line_comment_value1 == sam_v1_6_read_group_predicted_median_insert_size_value2++instance Show SAM_V1_6_Read_Group_Predicted_Median_Insert_Size where+  show (SAM_V1_6_Read_Group_Predicted_Median_Insert_Size tag value) =+    "SAM_V1_6_Read_Group_Predicted_Median_Insert_Size { " +++    "tag = "                                              +++    (show tag)                                            +++    " , value = "                                         +++    (show value)                                          +++    " }"++-- | PL tag for @"SAM_V1_6_Read_Group"@.+data SAM_V1_6_Read_Group_Platform = SAM_V1_6_Read_Group_Platform { sam_v1_6_read_group_platform_tag   :: Seq Word8+                                                                 , sam_v1_6_read_group_platform_value :: ByteString+                                                                 }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Read_Group_Platform where+  SAM_V1_6_Read_Group_Platform sam_v1_6_read_group_platform_tag1 sam_v1_6_read_group_platform_value1 == SAM_V1_6_Read_Group_Platform sam_v1_6_read_group_platform_tag2 sam_v1_6_read_group_platform_value2 = sam_v1_6_read_group_platform_tag1 == sam_v1_6_read_group_platform_tag2 && sam_v1_6_read_group_platform_value1 == sam_v1_6_read_group_platform_value2++instance Show SAM_V1_6_Read_Group_Platform where+  show (SAM_V1_6_Read_Group_Platform tag value) =+    "SAM_V1_6_Read_Group_Platform { " +++    "tag = "                          +++    (show tag)                        +++    " , value = "                     +++    (show value)                      +++    " }"++-- | PM tag for @"SAM_V1_6_Read_Group"@.+data SAM_V1_6_Read_Group_Platform_Model = SAM_V1_6_Read_Group_Platform_Model { sam_v1_6_read_group_platform_model_tag   :: Seq Word8+                                                                             , sam_v1_6_read_group_platform_model_value :: ByteString+                                                                             }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Read_Group_Platform_Model where+  SAM_V1_6_Read_Group_Platform_Model sam_v1_6_read_group_platform_model_tag1 sam_v1_6_read_group_platform_model_value1 == SAM_V1_6_Read_Group_Platform_Model sam_v1_6_read_group_platform_model_tag2 sam_v1_6_read_group_platform_model_value2 = sam_v1_6_read_group_platform_model_tag1 == sam_v1_6_read_group_platform_model_tag2 && sam_v1_6_read_group_platform_model_value1 == sam_v1_6_read_group_platform_model_value2++instance Show SAM_V1_6_Read_Group_Platform_Model where+  show (SAM_V1_6_Read_Group_Platform_Model tag value) =+    "SAM_V1_6_Read_Group_Platform_Model { " +++    "tag = "                                +++    (show tag)                              +++    " , value = "                           +++    (show value)                            +++    " }"++-- | PU tag for @"SAM_V1_6_Read_Group"@.+data SAM_V1_6_Read_Group_Platform_Unit = SAM_V1_6_Read_Group_Platform_Unit { sam_v1_6_read_group_platform_unit_tag   :: Seq Word8+                                                                           , sam_v1_6_read_group_platform_unit_value :: ByteString+                                                                           }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Read_Group_Platform_Unit where+  SAM_V1_6_Read_Group_Platform_Unit sam_v1_6_read_group_platform_unit_tag1 sam_v1_6_read_group_platform_unit_value1 == SAM_V1_6_Read_Group_Platform_Unit sam_v1_6_read_group_platform_unit_tag2 sam_v1_6_read_group_platform_unit_value2 = sam_v1_6_read_group_platform_unit_tag1 == sam_v1_6_read_group_platform_unit_tag2 && sam_v1_6_read_group_platform_unit_value1 == sam_v1_6_read_group_platform_unit_value2++instance Show SAM_V1_6_Read_Group_Platform_Unit where+  show (SAM_V1_6_Read_Group_Platform_Unit tag value) =+    "SAM_V1_6_Read_Group_Platform_Unit { " +++    "tag = "                               +++    (show tag)                             +++    " , value = "                          +++    (show value)                           +++    " }"++-- | SM tag for @"SAM_V1_6_Read_Group"@.+data SAM_V1_6_Read_Group_Sample = SAM_V1_6_Read_Group_Sample { sam_v1_6_read_group_sample_tag   :: Seq Word8+                                                             , sam_v1_6_read_group_sample_value :: ByteString+                                                             }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Read_Group_Sample where+  SAM_V1_6_Read_Group_Sample sam_v1_6_read_group_sample_tag1 sam_v1_6_read_group_sample_value1 == SAM_V1_6_Read_Group_Sample sam_v1_6_read_group_sample_tag2 sam_v1_6_read_group_sample_value2 = sam_v1_6_read_group_sample_tag1 == sam_v1_6_read_group_sample_tag2 && sam_v1_6_read_group_sample_value1 == sam_v1_6_read_group_sample_value2++instance Show SAM_V1_6_Read_Group_Sample where+  show (SAM_V1_6_Read_Group_Sample tag value) =+    "SAM_V1_6_Read_Group_Sample { " +++    "tag = "                        +++    (show tag)                      +++    " , value = "                   +++    (show value)                    +++    " }"
+ src/Data/SAM/Version1_6/Header/SQ.hs view
@@ -0,0 +1,271 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Header.SQ+-- 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.SAM.Version1_6.Header.SQ ( -- * SAM version 1.6 Reference sequence dictionary data type+                                       SAM_V1_6_Reference_Sequence_Dictionary(..),+                                       -- * SAM version 1.6 Reference sequence dictionary data types+                                       SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name(..),+                                       SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length(..),+                                       SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus(..),+                                       SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names(..),+                                       SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier(..),+                                       SAM_V1_6_Reference_Sequence_Dictionary_Description(..),+                                       SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum(..),+                                       SAM_V1_6_Reference_Sequence_Dictionary_Species(..),+                                       SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology(..),+                                       SAM_V1_6_Reference_Sequence_Dictionary_URI(..)+                                     ) where++import Data.ByteString+import Data.Data+import Data.Sequence+import Data.Word+import Generics.Deriving.Base++-- | Custom SAM (version 1.6) @"SAM_V1_6_Reference_Sequence_Dictionary"@ data type.+--+-- See section 1.3 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data SAM_V1_6_Reference_Sequence_Dictionary = SAM_V1_6_Reference_Sequence_Dictionary { sam_v1_6_reference_sequence_dictionary_reference_sequence_name                        :: SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name+                                                                                     , sam_v1_6_reference_sequence_dictionary_reference_sequence_length                      :: SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length+                                                                                     , sam_v1_6_reference_sequence_dictionary_reference_alternative_locus                    :: Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus+                                                                                     , sam_v1_6_reference_sequence_dictionary_reference_alternative_reference_sequence_names :: Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names+                                                                                     , sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier                     :: Maybe SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier+                                                                                     , sam_v1_6_reference_sequence_dictionary_description                                    :: Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description+                                                                                     , sam_v1_6_reference_sequence_dictionary_md5_checksum                                   :: Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum+                                                                                     , sam_v1_6_reference_sequence_dictionary_species                                        :: Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species+                                                                                     , sam_v1_6_reference_sequence_dictionary_molecule_topology                              :: Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology                                       +                                                                                     , sam_v1_6_reference_sequence_dictionary_uri                                            :: Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI +                                                                                     }+  deriving (Generic,Typeable)++instance Show SAM_V1_6_Reference_Sequence_Dictionary where+  show (SAM_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+       ) =+    "SAM_V1_6_Reference_Sequence_Dictionary { "  +++    "reference_sequence_name = "                 +++    (show reference_sequence_name)               +++    " , reference_sequence_length = "            +++    (show reference_sequence_length)             +++    " , reference_alternative_locus = "          +++    (show reference_alternative_locus)           +++    " , reference_alternative_sequence_names = " +++    (show reference_alternative_sequence_names)  +++    " , genome_assembly_identifier = "           +++    (show genome_assembly_identifier)            +++    " , description = "                          +++    (show description)                           +++    " , md5_checksum = "                         +++    (show md5_checksum)                          +++    " , species = "                              +++    (show species)                               +++    " , molecule_topology = "                    +++    (show molecule_topology)                     +++    " , uri = "                                  +++    (show uri)                                   +++    " }"++-- | SN tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@.+data SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name = SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name { sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tag   :: Seq Word8+                                                                                                                                     , sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value :: ByteString +                         }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name where+  SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tag1 sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tag2 sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value2 = sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tag1   == sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tag2 && sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value1 == sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value2  ++instance Show SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name where+  show (SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name tag value) =+    "SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name { " +++    "tag = "                                                            +++    (show tag)                                                          +++    " , value = "                                                       +++    (show value)                                                        +++    " }"++-- | LN tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@.+data SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length = SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length { sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tag   :: Seq Word8+                                                                                                                                         , sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value :: ByteString+                             }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length where+  SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tag1 sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tag2 sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value2 = sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tag1 == sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tag2 && sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value1 == sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value2++instance Show SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length where+  show (SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length tag value) =+    "SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length { " +++    "tag = "                                                              +++    (show tag)                                                            +++    " , value = "                                                         +++    (show value)                                                          +++    " }"++-- | AH tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@.+data SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus = SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus { sam_v1_6_reference_sequence_dictionary_alternative_locus_tag   :: Seq Word8+                                                                                                                         , sam_v1_6_reference_sequence_dictionary_alternative_locus_value :: ByteString+             }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus where+  SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus sam_v1_6_reference_sequence_dictionary_alternative_locus_tag1 sam_v1_6_reference_sequence_dictionary_alternative_locus_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus sam_v1_6_reference_sequence_dictionary_alternative_locus_tag2 sam_v1_6_reference_sequence_dictionary_alternative_locus_value2 = sam_v1_6_reference_sequence_dictionary_alternative_locus_tag1 == sam_v1_6_reference_sequence_dictionary_alternative_locus_tag2 && sam_v1_6_reference_sequence_dictionary_alternative_locus_value1 == sam_v1_6_reference_sequence_dictionary_alternative_locus_value2++instance Show SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus where+  show (SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus tag value) =+    "SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus { " +++    "tag = "                                                      +++    (show tag)                                                    +++    " , value = "                                                 +++    (show value)                                                  +++    " }"++-- | AN tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@.+data SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names = SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names { sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_tag   :: Seq Word8+                                                                                                                                                               , sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value :: ByteString+                                                                                                                                                               }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names where+  SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_tag1 sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_tag2 sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value2 = sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_tag1 == sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_tag2 && sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value1 == sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value2++instance Show SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names where+  show (SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names tag value) = "SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names { " +++                                                                                                 "tag = "                                                                         +++                                                                                                 (show tag)                                                                       +++                                                                                                 " , value = "                                                                    +++                                                                                                 (show value)                                                                     +++                                                                                                 " }"++-- | AS tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@.+data SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier = SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier { sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tag   :: Seq Word8+                                                                                                                                           , sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value :: ByteString+                                                                                                                                           }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier where+  SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tag1 sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tag2 sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value2 = sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tag1 == sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tag2 && sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value1 == sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value2++instance Show SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier where+  show (SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier tag value) = "SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier { " +++                                                                                       "tag = "                                                               +++                                                                                       (show tag)                                                             +++                                                                                       " , value = "                                                          +++                                                                                       (show value)                                                           +++                                                                                       " }"++-- | DS tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@.+data SAM_V1_6_Reference_Sequence_Dictionary_Description = SAM_V1_6_Reference_Sequence_Dictionary_Description { sam_v1_6_reference_sequence_dictionary_description_tag   :: Seq Word8+                                                                                                             , sam_v1_6_reference_sequence_dictionary_description_value :: ByteString+                                                                                                             }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Reference_Sequence_Dictionary_Description where+  SAM_V1_6_Reference_Sequence_Dictionary_Description sam_v1_6_reference_sequence_dictionary_description_tag1 sam_v1_6_reference_sequence_dictionary_description_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Description sam_v1_6_reference_sequence_dictionary_description_tag2 sam_v1_6_reference_sequence_dictionary_description_value2 = sam_v1_6_reference_sequence_dictionary_description_tag1 == sam_v1_6_reference_sequence_dictionary_description_tag2 && sam_v1_6_reference_sequence_dictionary_description_value1 == sam_v1_6_reference_sequence_dictionary_description_value2++instance Show SAM_V1_6_Reference_Sequence_Dictionary_Description where+  show (SAM_V1_6_Reference_Sequence_Dictionary_Description tag value) = "SAM_V1_6_Reference_Sequence_Dictionary_Description { " +++                                                                        "tag = "                                                +++                                                                        (show tag)                                              +++                                                                        " , value = "                                           +++                                                                        (show value)                                            +++                                                                        " }"++-- | M5 tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@.+data SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum = SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum { sam_v1_6_reference_sequence_dictionary_md5_checksum_tag   :: Seq Word8+                                                                                                               , sam_v1_6_reference_sequence_dictionary_md5_checksum_value :: ByteString+                                                                                                               }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum where+  SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum sam_v1_6_reference_sequence_dictionary_md5_checksum_tag1 sam_v1_6_reference_sequence_dictionary_md5_checksum_value1 == SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum sam_v1_6_reference_sequence_dictionary_md5_checksum_tag2 sam_v1_6_reference_sequence_dictionary_md5_checksum_value2 = sam_v1_6_reference_sequence_dictionary_md5_checksum_tag1 == sam_v1_6_reference_sequence_dictionary_md5_checksum_tag2 && sam_v1_6_reference_sequence_dictionary_md5_checksum_value1 == sam_v1_6_reference_sequence_dictionary_md5_checksum_value2++instance Show SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum where+  show (SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum tag value) = "SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum { " +++                                                                         "tag = "                                                 +++                                                                         (show tag)                                               +++                                                                         " , value = "                                            +++                                                                         (show value)                                             +++                                                                         " }"++-- | SP tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@.+data SAM_V1_6_Reference_Sequence_Dictionary_Species = SAM_V1_6_Reference_Sequence_Dictionary_Species { sam_v1_6_reference_sequence_dictionary_species_tag   :: Seq Word8+                                                                                                     , sam_v1_6_reference_sequence_dictionary_species_value :: ByteString+                                                                                                     }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Reference_Sequence_Dictionary_Species where+  SAM_V1_6_Reference_Sequence_Dictionary_Species sam_v1_6_reference_sequence_dictionary_species_tag1 sam_v1_6_reference_sequence_dictionary_species_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Species sam_v1_6_reference_sequence_dictionary_species_tag2 sam_v1_6_reference_sequence_dictionary_species_value2 = sam_v1_6_reference_sequence_dictionary_species_tag1 == sam_v1_6_reference_sequence_dictionary_species_tag2 && sam_v1_6_reference_sequence_dictionary_species_value1 == sam_v1_6_reference_sequence_dictionary_species_value2++instance Show SAM_V1_6_Reference_Sequence_Dictionary_Species where+  show (SAM_V1_6_Reference_Sequence_Dictionary_Species tag value) =+    "SAM_V1_6_Reference_Sequence_Dictionary_Species { " +++    "tag = "                                            +++    (show tag)                                          +++    " , value = "                                       +++    (show value)                                        +++    " }"++-- | TP tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@.+data SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology = SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology { sam_v1_6_reference_sequence_dictionary_molecule_topology_tag   :: Seq Word8+                                                                                                                         , sam_v1_6_reference_sequence_dictionary_molecule_topology_value :: ByteString+                                                                                                                         }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology where+  SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology sam_v1_6_reference_sequence_dictionary_molecule_topology_tag1 sam_v1_6_reference_sequence_dictionary_molecule_topology_value1 == SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology sam_v1_6_reference_sequence_dictionary_molecule_topology_tag2 sam_v1_6_reference_sequence_dictionary_molecule_topology_value2 = sam_v1_6_reference_sequence_dictionary_molecule_topology_tag1 == sam_v1_6_reference_sequence_dictionary_molecule_topology_tag2 && sam_v1_6_reference_sequence_dictionary_molecule_topology_value1 == sam_v1_6_reference_sequence_dictionary_molecule_topology_value2++instance Show SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology where+  show (SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology tag value) =+    "SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology { " +++    "tag = "                                                      +++    (show tag)                                                    +++    " , value = "                                                 +++    (show value)                                                  +++    " }"++-- | UR tag for @"SAM_V1_6_Reference_Sequence_Dictionary"@.+data SAM_V1_6_Reference_Sequence_Dictionary_URI = SAM_V1_6_Reference_Sequence_Dictionary_URI { sam_v1_6_reference_sequence_dictionary_uri_tag   :: Seq Word8+                                                                                             , sam_v1_6_reference_sequence_dictionary_uri_value :: ByteString+                                                                                             }+  deriving (Generic,Typeable)++instance Eq SAM_V1_6_Reference_Sequence_Dictionary_URI where+  SAM_V1_6_Reference_Sequence_Dictionary_URI sam_v1_6_reference_sequence_dictionary_uri_tag1 sam_v1_6_reference_sequence_dictionary_uri_value1 == SAM_V1_6_Reference_Sequence_Dictionary_URI sam_v1_6_reference_sequence_dictionary_uri_tag2 sam_v1_6_reference_sequence_dictionary_uri_value2 = sam_v1_6_reference_sequence_dictionary_uri_tag1 == sam_v1_6_reference_sequence_dictionary_uri_tag2 && sam_v1_6_reference_sequence_dictionary_uri_value1 == sam_v1_6_reference_sequence_dictionary_uri_value2++instance Show SAM_V1_6_Reference_Sequence_Dictionary_URI where+  show (SAM_V1_6_Reference_Sequence_Dictionary_URI tag value) =+    "SAM_V1_6_Reference_Sequence_Dictionary_URI { " +++    "tag = "                                        +++    (show tag)                                      +++    " , value = "                                   +++    (show value)                                    +++    " }"
+ src/Data/SAM/Version1_6/Read/Base.hs view
@@ -0,0 +1,97 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.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.SAM.Version1_6.Read.Base ( -- * Reading+                                       readSAM_V1_6+                                     ) where++import Data.SAM.Version1_6.Base+import Data.SAM.Version1_6.Read.Parser.Header.HD.Base+import Data.SAM.Version1_6.Read.Parser.Header.SQ.Base+import Data.SAM.Version1_6.Read.Parser.Header.RG.Base+import Data.SAM.Version1_6.Read.Parser.Header.PG.Base+import Data.SAM.Version1_6.Read.Parser.Header.CO.Base+import Data.SAM.Version1_6.Read.Parser.Alignment.Base++import Data.Attoparsec.ByteString.Char8  as DABC8+import Data.Attoparsec.ByteString.Lazy   as DABL+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)++-- | Make a parser optional, return Nothing if there is no match.+maybeOption :: Parser a+            -> Parser (Maybe a)+maybeOption p = option Nothing (Just <$> p)++-- | Define the @"SAM_V1_6"@ parser.+parse_SAM_V1_6 :: Parser SAM_V1_6+parse_SAM_V1_6 = do+  filelevelmetadata           <- maybeOption $ parse_SAM_V1_6_File_Level_Metadata <* endOfLine+  _                           <- word8 10+  referencesequencedictionary <- maybeOption $ DABL.many' $ parse_SAM_V1_6_Reference_Sequence_Dictionary <* endOfLine+  _                           <- word8 10+  readgroup                   <- maybeOption $ DABL.many' $ parse_SAM_V1_6_Read_Group <* endOfLine+  _                           <- word8 10+  program                     <- maybeOption $ parse_SAM_V1_6_Program <* endOfLine+  _                           <- word8 10+  onelinecomment              <- maybeOption $ DABL.many' $ parse_SAM_V1_6_One_Line_Comment <* endOfLine +  _                           <- word8 10+  alignment                   <- DABL.many' $ parse_SAM_V1_6_Alignment <* endOfLine+  return SAM_V1_6 { sam_v1_6_file_level_metadata           = filelevelmetadata+                  , sam_v1_6_reference_sequence_dictionary = case referencesequencedictionary of+                                                               Nothing                           -> Nothing+                                                               Just referencesequencedictionaryf -> Just $ DSeq.fromList referencesequencedictionaryf+                  , sam_v1_6_read_group                    = case readgroup of+                                                               Nothing         -> Nothing+                                                               Just readgroupf -> Just $ DSeq.fromList readgroupf+                  , sam_v1_6_program                       = program+                  , sam_v1_6_one_line_comment              = case onelinecomment of+                                                               Nothing              -> Nothing+                                                               Just onelinecommentf -> Just $ DSeq.fromList onelinecommentf+                  , sam_v1_6_alignment                     = DSeq.fromList alignment+                  } ++-- | Run the @"SAM_V1_6"@ parser.+readSAM_V1_6_LBS :: DBL.ByteString+                 -> IO SAM_V1_6+readSAM_V1_6_LBS lbs =+  case (DABL.parseOnly parse_SAM_V1_6 lbs) of+    Left  samparseerror -> error samparseerror+    Right sam           -> return sam++-- | Read a @"SAM_V1_6"@ from a file.+--+-- The file is checked for errors as it parses the SAM file.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+readSAM_V1_6 :: FilePath -- ^ Path to SAM file.+             -> IO SAM_V1_6+readSAM_V1_6 fp = do+  let lazysamfile = S.unfold StreamlyInternalFile.chunkReader fp+  lazysamfilef    <- StreamlyLByteString.fromChunksIO lazysamfile+  readSAM_V1_6_LBS lazysamfilef
+ src/Data/SAM/Version1_6/Read/Error.hs view
@@ -0,0 +1,241 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Error+-- 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.SAM.Version1_6.Read.Error ( -- * SAM version 1.6 data type+                                        SAM_V1_6_Error(..)+                                      ) where++import Data.Data+import Generics.Deriving.Base++-- | Custom @"SAM_V1_6"@ (SAM version 1.6) error data type.+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+data SAM_V1_6_Error = -- | @HD tag not in accepted format (only important+                      -- if @HD tag is present).+                      SAM_V1_6_Error_File_Level_Metadata_Tag_Incorrect_Format+                      -- | VN tag missing (only important+                      -- if @HD tag is present).+                    | SAM_V1_6_Error_File_Level_Metadata_Format_Version_Tag_Missing+                      -- | VN tag not in accepted format (only important+                      -- if @HD tag is present).+                    | SAM_V1_6_Error_File_Level_Metadata_Format_Version_Tag_Incorrect_Format+                      -- | VN value not in accepted format (only important+                      -- if @HD tag is present).+                    | SAM_V1_6_Error_File_Level_Metadata_Format_Version_Value_Incorrect_Format+                      -- | Sorting order tag not in accepted format (only important+                      -- if @HD tag is present).+                    | SAM_V1_6_Error_File_Level_Metadata_Sorting_Order_Tag_Incorrect_Format+                      -- | Sorting order invalid value (only important+                      -- if @HD tag is present).+                    | SAM_V1_6_Error_File_Level_Metadata_Sorting_Order_Invalid_Value+                      -- | Grouping of alignments no in accepted format (only important+                      -- if @HD tag is present).+                    | SAM_V1_6_Error_File_Level_Metadata_Grouping_Of_Alignments_Tag_Incorrect_Format+                      -- | Grouping of Alignments invalid value (only important+                      -- if @HD tag is present).+                    | SAM_V1_6_Error_File_Level_Metadata_Grouping_Of_Alignments_Invalid_Value+                      -- | Subsorting order tag not in accepted format (only important+                      -- if @HD tag is present).+                    | SAM_V1_6_Error_File_Level_Metadata_Subsorting_Order_Tag_Incorrect_Format+                      -- | Subsorting order of alignments not in accepted format (only+                      -- if @HD tag is present.+                    | SAM_V1_6_Error_File_Level_Metadata_Subsorting_Order_Incorrect_Format+                      -- | SN tag missing (only important+                      -- if @SQ tag is present).+                    | SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Name_Tag_Missing+                      -- | Reference Sequence Name not in accepted format (only important+                      -- if @SQ tag is present.+                    | SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Name_Incorrect_Format+                      -- | Reference Sequence Name invalid value (only important+                      -- if @SQ tag is present).+                    | SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Name_Invalid_Value+                      -- | LN tag missing (only important+                      -- if @SQ tag is present).+                    |  SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Length_Missing+                      -- | Reference Sequence Length not in accepted format (only important+                      -- if @SQ tag is present.+                    | SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Length_Incorrect_Format+                      -- | Reference Sequence Length invalid value (only important+                      -- if @SQ tag is present).+                    | SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Length_Invalid_Value+                      -- | Alternative locus not in accepted format (only important+                      -- if @SQ tag is present).+                    | SAM_V1_6_Error_Reference_Sequence_Dictionary_Alternative_Locus_Incorrect_Format+                      -- | Alternative Reference Sequence Names not in accepted format (only important+                      -- if @SQ tag is present).+                    | SAM_V1_6_Error_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names_Incorrect_Format+                      -- | Alternative Reference Sequence Names invalid value (only important+                      -- if @SQ tag is present).+                    | SAM_V1_6_Error_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names_Invalid_Value+                      -- | Genome Assembly Identifier not in accepted format (only important+                      -- if @SQ tag is present).+                    | SAM_V1_6_Error_Reference_Sequence_Dictionary_Genome_Assembly_Identifier_Incorrect_Format+                      -- | Description not in accepted format (only important+                      -- if @SQ tag is present).+                    | SAM_V1_6_Error_Reference_Sequence_Dictionary_Description_Incorrect_Format+                      -- | MD5 checksum not in accepted format (only important+                      -- if @SQ tag is present).+                    | SAM_V1_6_Error_Reference_Sequence_Dictionary_MD5_Checksum_Incorrect_Format+                      -- | Species not in accepted format (only important+                      -- if @SQ tag is present).+                    | SAM_V1_6_Error_Reference_Sequence_Dictionary_Species_Incorrect_Format+                      -- | Molecule topology not in accepted format (only important+                      -- if @SQ tag is present).+                    | SAM_V1_6_Error_Reference_Sequence_Dictionary_Molecule_Topology_Incorrect_Format+                      -- | Molecule topology invalid value (only important+                      -- if @SQ tag is present).+                    | SAM_V1_6_Error_Reference_Sequence_Dictionary_Molecule_Topology_Invalid_Value+                      -- | URI not in accepted format (only important+                      -- if @SQ tag is present).+                    | SAM_V1_6_Error_Reference_Sequence_Dictionary_URI_Incorrect_Format+                      -- | ID tag not accepted format (only important+                      -- if @RG tag is present).+                    | SAM_V1_6_Error_Read_Group_Read_Group_Identifier_Incorrect_Format+                      -- | ID tag is missing (only important+                      -- if @RG tag is present).+                    | SAM_V1_6_Error_Read_Group_Read_Group_Identifier_Tag_Missing+                      -- | BC tag not in accepted format (only important+                      -- if @RG tag is present).+                    | SAM_V1_6_Error_Read_Group_Barcode_Sequence_Incorrect_Format+                      -- | CN tag not in accepted format (only important+                      -- if @RG tag is present).+                    | SAM_V1_6_Error_Read_Group_Sequencing_Center_Incorrect_Format+                      -- | DS tag not in accepted format (only important+                      -- if @RG tag is present).+                    | SAM_V1_6_Error_Read_Group_Description_Incorrect_Format+                      -- | DT tag not in accepted format (only important+                      -- if @RG tag is present).+                    | SAM_V1_6_Error_Read_Group_Date_Run_Produced_Incorrect_Format+                      -- | FO tag not in accepted format (only important+                      -- if @RG tag is present).+                    | SAM_V1_6_Error_Read_Group_Flow_Order_Incorrect_Format+                      -- | KS tag not in accepted format (only important+                      -- if @RG tag is present).+                    | SAM_V1_6_Error_Read_Group_Key_Sequence_Incorrect_Format+                      -- | LB tag not in accepted format (only important+                      -- if @RG tag is present).+                    | SAM_V1_6_Error_Read_Group_Library_Incorrect_Format+                      -- | PG tag not in accepted format (only important+                      -- if @RG tag is present).+                    | SAM_V1_6_Error_Read_Group_Programs_Incorrect_Format+                      -- | PI tag not in accepted format (only important+                      -- if @RG tag is present).+                    | SAM_V1_6_Error_Read_Group_Predicted_Median_Insert_Size_Incorrect_Format+                      -- | PL tag not in accepted format (only important+                      -- if @RG tag is present).+                    | SAM_V1_6_Error_Read_Group_Platform_Incorrect_Format+                      -- | PM tag not in accepted format (only important+                      -- if @RG tag is present).+                    | SAM_V1_6_Error_Read_Group_Platform_Model_Incorrect_Format+                      -- | PU tag not in accepted format (only important+                      -- if @RG tag is present).+                    | SAM_V1_6_Error_Read_Group_Platform_Unit_Incorrect_Format+                      -- | SM tag not in accepted format (only important+                      -- if @RG tag is present).+                    | SAM_V1_6_Error_Read_Group_Sample_Incorrect_Format+                      -- | RG tag not in accepted format.+                    | SAM_V1_6_Error_Read_Group_Tag_Incorrect_Format+                      -- | ID tag not in accepted format (only important+                      -- if @PG tag is present).+                    | SAM_V1_6_Error_Program_Identifier_Incorrect_Format+                      -- | PN tag not in accepted format (only important+                      -- if @PG tag is present).+                    | SAM_V1_6_Error_Program_Name_Incorrect_Format+                      -- | CL tag not in accepted format (only important+                      -- if @PG tag is present).+                    | SAM_V1_6_Error_Program_Command_Line_Incorrect_Format+                      -- | PP tag not in accepted format (only important+                      -- if @PG tag is present).+                    | SAM_V1_6_Error_Program_Previous_PG_ID_Incorrect_Format+                      -- | DS tag not in accepted format (only important+                      -- if @PG tag is present).+                    | SAM_V1_6_Error_Program_Description_Incorrect_Format+                      -- | VN tag not in accepted format (only important+                      -- if @PG tag is present).+                    | SAM_V1_6_Error_Program_Version_Incorrect_Format+                      -- | PG tag not in accepted format.+                    | SAM_V1_6_Error_Program_Tag_Incorrect_Format+                      -- | CO tag not in accepted format.+                    | SAM_V1_6_Error_One_Line_Comment_Tag_Incorrect_Format+                      -- | QNAME of alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_QNAME_Incorrect_Format+                      -- | FLAG of alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_FLAG_Incorrect_Format+                      -- | RNAME of alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_RNAME_Incorrect_Format+                      -- | POS of alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_POS_Incorrect_Format+                      -- | MAPQ of alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_MAPQ_Incorrect_Format+                      -- | CIGAR of alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_CIGAR_Incorrect_Format+                      -- | RNEXT of alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_RNEXT_Incorrect_Format+                      -- | PNEXT of alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_PNEXT_Incorrect_Format+                      -- | TLEN of alignment section not in accpepted format.+                    | SAM_V1_6_Error_Alignment_TLEN_Incorrect_Format+                      -- | SEQ of alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_SEQ_Incorrect_Format+                      -- | QUAL of alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_QUAL_Incorrect_Format+                      -- | AOPT tag of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_AOPT_Tag_Incorrect_Format+                      -- | AOPT type of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_AOPT_Type_Incorrect_Format+                      -- | AOPT value of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_AOPT_Value_Incorrect_Format+                      -- | IOPT tag of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_IOPT_Tag_Incorrect_Format+                      -- | IOPT type of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_IOPT_Type_Incorrect_Format+                      -- | IOPT value of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_IOPT_Value_Incorrect_Format+                      -- | FOPT tag of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_FOPT_Tag_Incorrect_Format+                      -- | FOPT type of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_FOPT_Type_Incorrect_Format+                      -- | FOPT value of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_FOPT_Value_Incorrect_Format+                      -- | ZOPT tag of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_ZOPT_Tag_Incorrect_Format+                      -- | ZOPT type of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_ZOPT_Type_Incorrect_Format+                      -- | ZOPT value of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_ZOPT_Value_Incorrect_Format+                      -- | HOPT tag of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_HOPT_Tag_Incorrect_Format+                      -- | HOPT type of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_HOPT_Type_Incorrect_Format+                      -- | HOPT value of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_HOPT_Value_Incorrect_Format+                      -- | BOPT tag of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_BOPT_Tag_Incorrect_Format+                      -- | BOPT type of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_BOPT_Type_Incorrect_Format+                      -- | BOPT value type of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_BOPT_Value_Type_Incorrect_Format+                      -- | BOPT value data of the alignment section not in accepted format.+                    | SAM_V1_6_Error_Alignment_BOPT_Value_Data_Incorrect_Format+  deriving (Eq,Generic,Show,Typeable)
+ src/Data/SAM/Version1_6/Read/Parser/Alignment/AOPT.hs view
@@ -0,0 +1,78 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Alignment.AOPT+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Alignment.AOPT ( -- * SAM_V1_6 parser - alignment section - aopt field +                                                        parse_SAM_V1_6_Alignment_AOPT+                                                      ) where++import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the optional aopt field of alignment section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_Alignment_AOPT :: Parser DB.ByteString+parse_SAM_V1_6_Alignment_AOPT = do+  _ <- do alignmentaoptfieldtagp <- DABL.takeTill (== 58)+          -- Parse AOPT tag of the alignment section.+          case (alignmentaoptfieldtagp =~ [re|/[A-Za-z][A-Za-z0-9]/|]) of+            False -> fail $ show SAM_V1_6_Error_Alignment_AOPT_Tag_Incorrect_Format+            True  -> -- AOPT tag is in the accepted format. +                     return alignmentaoptfieldtagp+  _ <- word8 58+  _ <- do alignmentaoptfieldtypep <- DABL.takeTill (== 58)+          -- Parse AOPT type of the alignment section.+          case (alignmentaoptfieldtypep =~ [re|[A]|]) of+            False -> fail $ show SAM_V1_6_Error_Alignment_AOPT_Type_Incorrect_Format+            True  -> -- AOPT type is in the accepted format.+                     return alignmentaoptfieldtypep+  _ <- word8 58+  alignmentaoptfieldvalue <- do alignmentaoptfieldvaluep <- DABL.takeTill (== 09)+                                -- Parse AOPT value of the alignment section.+                                case (alignmentaoptfieldvaluep =~ [re|[!-~]|]) of+                                  False -> fail $ show SAM_V1_6_Error_Alignment_AOPT_Value_Incorrect_Format+                                  True  -> -- AOPT value is in the accepted format.+                                           return alignmentaoptfieldvaluep+  return alignmentaoptfieldvalue
+ src/Data/SAM/Version1_6/Read/Parser/Alignment/BOPT.hs view
@@ -0,0 +1,172 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Alignment.BOPT+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Alignment.BOPT ( -- * SAM_V1_6 parser - alignment section - bopt field +                                                        parse_SAM_V1_6_Alignment_BOPT+                                                      ) where++import Data.SAM.Version1_6.Alignment.BOPT+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB (head,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 SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_Alignment_BOPT :: Parser SAM_V1_6_Alignment_BOPT+parse_SAM_V1_6_Alignment_BOPT = do+  alignmentboptfieldtag <- do alignmentboptfieldtagp <- DABL.takeTill (== 58)+                              -- Parse BOPT tag of the alignment section.+                              case (alignmentboptfieldtagp =~ [re|/[A-Za-z][A-Za-z0-9]/|]) of+                                False -> fail $ show SAM_V1_6_Error_Alignment_BOPT_Tag_Incorrect_Format+                                True  -> -- BOPT tag is in the accepted format. +                                         return alignmentboptfieldtagp+  _ <- word8 58+  _ <- do alignmentboptfieldtypep <- DABL.takeTill (== 58)+          -- Parse BOPT type of the alignment section.+          case (alignmentboptfieldtypep =~ [re|[B]|]) of+            False -> fail $ show SAM_V1_6_Error_Alignment_BOPT_Type_Incorrect_Format+            True  -> -- BOPT type is in the accepted format.+                     return alignmentboptfieldtypep+  _ <- word8 58+  alignmentboptfieldvaluetype <- do alignmentboptfieldvaluetypep <- DABL.take 1+                                    -- Parse BOPT value type of the alignment section.+                                    case (alignmentboptfieldvaluetypep =~ [re|[cCsSiIf]|]) of+                                      False -> fail $ show SAM_V1_6_Error_Alignment_BOPT_Value_Type_Incorrect_Format+                                      True  -> -- BOPT value type is in the accepted format.+                                               return alignmentboptfieldvaluetypep+  alignmentboptfieldvaluedata <- do alignmentboptfieldvaluedatap <- DABL.takeTill (\x -> x == 09 || x == 0x0D || x == 0x0A)+                                    -- Parse BOPT value data of the alignment section.+                                    case (alignmentboptfieldvaluedatap =~ [re|(,[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)*|]) of+                                      False -> fail $ show SAM_V1_6_Error_Alignment_BOPT_Value_Data_Incorrect_Format+                                      True  -> -- BOPT value data is in the accepted format.+                                               return alignmentboptfieldvaluedatap+  case (DBC8.unpack alignmentboptfieldvaluetype) of+    "c" -> return SAM_V1_6_Alignment_BOPT { sam_v1_6_alignment_bopt_int8   = Just SAM_V1_6_Alignment_BOPT_Int8 { sam_v1_6_alignment_bopt_int8_tag   = DSeq.fromList $ DB.unpack alignmentboptfieldtag+                                                                                                               , sam_v1_6_alignment_bopt_int8_type  = DB.head alignmentboptfieldvaluetype+                                                                                                               , sam_v1_6_alignment_bopt_int8_value = fmap fromIntegral (DSeq.fromList $ DB.unpack alignmentboptfieldvaluedata)+                                                                                                               }+                                          , sam_v1_6_alignment_bopt_word8  = Nothing+                                          , sam_v1_6_alignment_bopt_int16  = Nothing+                                          , sam_v1_6_alignment_bopt_word16 = Nothing+                                          , sam_v1_6_alignment_bopt_int32  = Nothing+                                          , sam_v1_6_alignment_bopt_word32 = Nothing+                                          , sam_v1_6_alignment_bopt_float  = Nothing+                                          }+    "C" -> return SAM_V1_6_Alignment_BOPT { sam_v1_6_alignment_bopt_int8   = Nothing+                                          , sam_v1_6_alignment_bopt_word8  = Just SAM_V1_6_Alignment_BOPT_Word8 { sam_v1_6_alignment_bopt_word8_tag   = DSeq.fromList $ DB.unpack alignmentboptfieldtag+                                                                                                                , sam_v1_6_alignment_bopt_word8_type  = DB.head alignmentboptfieldvaluetype+                                                                                                                , sam_v1_6_alignment_bopt_word8_value = DSeq.fromList $ DB.unpack alignmentboptfieldvaluedata+                                                                                                                } +                                          , sam_v1_6_alignment_bopt_int16  = Nothing+                                          , sam_v1_6_alignment_bopt_word16 = Nothing+                                          , sam_v1_6_alignment_bopt_int32  = Nothing+                                          , sam_v1_6_alignment_bopt_word32 = Nothing+                                          , sam_v1_6_alignment_bopt_float  = Nothing+                                          }+    "s" -> return SAM_V1_6_Alignment_BOPT { sam_v1_6_alignment_bopt_int8   = Nothing+                                          , sam_v1_6_alignment_bopt_word8  = Nothing+                                          , sam_v1_6_alignment_bopt_int16  = Just SAM_V1_6_Alignment_BOPT_Int16 { sam_v1_6_alignment_bopt_int16_tag   = DSeq.fromList $ DB.unpack alignmentboptfieldtag+                                                                                                                , sam_v1_6_alignment_bopt_int16_type  = DB.head alignmentboptfieldvaluetype+                                                                                                                , sam_v1_6_alignment_bopt_int16_value = fmap fromIntegral (DSeq.fromList $ DB.unpack alignmentboptfieldvaluedata)+                                                                                                                }+                                          , sam_v1_6_alignment_bopt_word16 = Nothing+                                          , sam_v1_6_alignment_bopt_int32  = Nothing+                                          , sam_v1_6_alignment_bopt_word32 = Nothing+                                          , sam_v1_6_alignment_bopt_float  = Nothing+                                          }+    "S" -> return SAM_V1_6_Alignment_BOPT { sam_v1_6_alignment_bopt_int8   = Nothing+                                          , sam_v1_6_alignment_bopt_word8  = Nothing+                                          , sam_v1_6_alignment_bopt_int16  = Nothing+                                          , sam_v1_6_alignment_bopt_word16 = Just SAM_V1_6_Alignment_BOPT_Word16 { sam_v1_6_alignment_bopt_word16_tag   = DSeq.fromList $ DB.unpack alignmentboptfieldtag+                                                                                                                 , sam_v1_6_alignment_bopt_word16_type  = DB.head alignmentboptfieldvaluetype+                                                                                                                 , sam_v1_6_alignment_bopt_word16_value = fmap fromIntegral (DSeq.fromList $ DB.unpack alignmentboptfieldvaluedata)+                                                                                                                 }+                                          , sam_v1_6_alignment_bopt_int32  = Nothing+                                          , sam_v1_6_alignment_bopt_word32 = Nothing+                                          , sam_v1_6_alignment_bopt_float  = Nothing+                                          }+    "i" -> return SAM_V1_6_Alignment_BOPT { sam_v1_6_alignment_bopt_int8   = Nothing+                                          , sam_v1_6_alignment_bopt_word8  = Nothing+                                          , sam_v1_6_alignment_bopt_int16  = Nothing+                                          , sam_v1_6_alignment_bopt_word16 = Nothing+                                          , sam_v1_6_alignment_bopt_int32  = Just SAM_V1_6_Alignment_BOPT_Int32 { sam_v1_6_alignment_bopt_int32_tag   = DSeq.fromList $ DB.unpack alignmentboptfieldtag+                                                                                                                , sam_v1_6_alignment_bopt_int32_type  = DB.head alignmentboptfieldvaluetype+                                                                                                                , sam_v1_6_alignment_bopt_int32_value = fmap fromIntegral (DSeq.fromList $ DB.unpack alignmentboptfieldvaluedata)+                                                                                                                }+                                          , sam_v1_6_alignment_bopt_word32 = Nothing+                                          , sam_v1_6_alignment_bopt_float  = Nothing+                                          }+    "I" -> return SAM_V1_6_Alignment_BOPT { sam_v1_6_alignment_bopt_int8   = Nothing+                                          , sam_v1_6_alignment_bopt_word8  = Nothing+                                          , sam_v1_6_alignment_bopt_int16  = Nothing+                                          , sam_v1_6_alignment_bopt_word16 = Nothing+                                          , sam_v1_6_alignment_bopt_int32  = Nothing+                                          , sam_v1_6_alignment_bopt_word32 = Just SAM_V1_6_Alignment_BOPT_Word32 { sam_v1_6_alignment_bopt_word32_tag   = DSeq.fromList $ DB.unpack alignmentboptfieldtag+                                                                                                                 , sam_v1_6_alignment_bopt_word32_type  = DB.head alignmentboptfieldvaluetype+                                                                                                                 , sam_v1_6_alignment_bopt_word32_value = fmap fromIntegral (DSeq.fromList $ DB.unpack alignmentboptfieldvaluedata)+                                                                                                                 }+                                          , sam_v1_6_alignment_bopt_float  = Nothing+                                          }+    "f" -> return SAM_V1_6_Alignment_BOPT { sam_v1_6_alignment_bopt_int8   = Nothing+                                          , sam_v1_6_alignment_bopt_word8  = Nothing+                                          , sam_v1_6_alignment_bopt_int16  = Nothing+                                          , sam_v1_6_alignment_bopt_word16 = Nothing+                                          , sam_v1_6_alignment_bopt_int32  = Nothing+                                          , sam_v1_6_alignment_bopt_word32 = Nothing+                                          , sam_v1_6_alignment_bopt_float  = Just SAM_V1_6_Alignment_BOPT_Float { sam_v1_6_alignment_bopt_float_tag   = DSeq.fromList $ DB.unpack alignmentboptfieldtag+                                                                                                                , sam_v1_6_alignment_bopt_float_type  = DB.head alignmentboptfieldvaluetype+                                                                                                                , sam_v1_6_alignment_bopt_float_value = fmap fromIntegral (DSeq.fromList $ DB.unpack alignmentboptfieldvaluedata)+                                                                                                                }+                                          }+    _   -> return SAM_V1_6_Alignment_BOPT { sam_v1_6_alignment_bopt_int8   = Nothing+                                          , sam_v1_6_alignment_bopt_word8  = Nothing+                                          , sam_v1_6_alignment_bopt_int16  = Nothing+                                          , sam_v1_6_alignment_bopt_word16 = Nothing+                                          , sam_v1_6_alignment_bopt_int32  = Nothing+                                          , sam_v1_6_alignment_bopt_word32 = Nothing+                                          , sam_v1_6_alignment_bopt_float  = Nothing+                                          }
+ src/Data/SAM/Version1_6/Read/Parser/Alignment/Base.hs view
@@ -0,0 +1,191 @@+{-# LANGUAGE DeriveDataTypeable          #-}+{-# LANGUAGE DeriveGeneric               #-}+{-# LANGUAGE FlexibleContexts            #-}+{-# LANGUAGE FlexibleInstances           #-}+{-# LANGUAGE MultiParamTypeClasses       #-}+{-# LANGUAGE OverloadedLists             #-}+{-# LANGUAGE OverloadedStrings           #-}+{-# LANGUAGE MultiWayIf                  #-}+{-# LANGUAGE PackageImports              #-}+{-# LANGUAGE RecordWildCards             #-}+{-# LANGUAGE TemplateHaskell             #-}+{-# LANGUAGE TypeFamilies                #-}+{-# Language QuasiQuotes                 #-}+{-# OPTIONS_GHC -fno-warn-name-shadowing #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Alignment.Base+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Alignment.Base ( -- * SAM_V1_6 parser - alignment section+                                                        parse_SAM_V1_6_Alignment+                                                      ) where++import Data.SAM.Version1_6.Alignment+import Data.SAM.Version1_6.Read.Error+import Data.SAM.Version1_6.Read.Parser.Alignment.AOPT+import Data.SAM.Version1_6.Read.Parser.Alignment.IOPT+import Data.SAM.Version1_6.Read.Parser.Alignment.FOPT+import Data.SAM.Version1_6.Read.Parser.Alignment.ZOPT+import Data.SAM.Version1_6.Read.Parser.Alignment.HOPT+import Data.SAM.Version1_6.Read.Parser.Alignment.BOPT++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString.Char8             as DBC8+import           Text.Regex.PCRE.Heavy++-- | Make a parser optional, return Nothing if there is no match.+maybeOption :: Parser a+            -> Parser (Maybe a)+maybeOption p = option Nothing (Just <$> p)++-- | @"SAM_V1_6_Alignment"@ parser.+--+-- Defines a parser for the alignment section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_Alignment :: Parser SAM_V1_6_Alignment+parse_SAM_V1_6_Alignment = do+  qname <- do qnamep <- DABL.takeTill (== 09)+              -- Parse QNAME field of alignment section.+              case (qnamep =~ [re|[!-?A-~]{1,254}|\*|]) of+                False -> fail $ show SAM_V1_6_Error_Alignment_QNAME_Incorrect_Format+                True  -> -- QNAME is in the accepted format.+                         return qnamep+  _ <- word8 09+  flag <- do flagp <- DABL.takeTill (== 09)+             -- Parse FLAG field of alignment section.+             case (flagp =~ [re|[0-9]*|]) of+               False -> fail $ show SAM_V1_6_Error_Alignment_FLAG_Incorrect_Format+               True  -> -- FLAG is in the accepted format.+                        return flagp+  _ <- word8 09+  rname <- do rnamep <- DABL.takeTill (== 09)+              -- Parse RNAME field of alignment section.+              case (rnamep =~ [re|\*|[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*|]) of+                False -> fail $ show SAM_V1_6_Error_Alignment_RNAME_Incorrect_Format +                True  -> -- RNAME is in the accepted format.+                         return rnamep+  _ <- word8 09+  pos <- do posp <- DABL.takeTill (== 09)+            -- Parse POS field of the alignment section.+            case (posp =~ [re|[0-9]*|]) of+              False -> fail $ show SAM_V1_6_Error_Alignment_POS_Incorrect_Format+              True  -> -- POS is in the accepted format.+                       return posp+  _ <- word8 09+  mapq <- do mapqp <- DABL.takeTill (== 09)+             -- Parse MAPQ field of the alignment section.+             case (mapqp =~ [re|[0-9]*|]) of+               False -> fail $ show SAM_V1_6_Error_Alignment_MAPQ_Incorrect_Format+               True  -> -- MAPQ is in the accepted format.+                        return mapqp+  _ <- word8 09+  cigar <- do cigarp <- DABL.takeTill (== 09)+              -- Parse CIGAR field of alignment section.+              case (cigarp =~ [re|\*|([0-9]+[MIDNSHPX=])+|]) of+                False -> fail $ show SAM_V1_6_Error_Alignment_CIGAR_Incorrect_Format+                True  -> -- CIGAR is in the accepted format.+                         return cigarp+  _ <- word8 09+  rnext <- do rnextp <- DABL.takeTill (== 09)+              -- Parse RNEXT field of the alignment section.+              case (rnextp =~ [re|\*|=|[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*|]) of+                False -> fail $ show SAM_V1_6_Error_Alignment_RNEXT_Incorrect_Format+                True  -> -- RNEXT is in the accepted format.+                         return rnextp+  _ <- word8 09+  pnext <- do pnextp <- DABL.takeTill (== 09)+              -- Parse PNEXT field of the alignment section.+              case (pnextp =~ [re|[0-9]*|]) of+                False -> fail $ show SAM_V1_6_Error_Alignment_PNEXT_Incorrect_Format+                True  -> -- PNEXT is in the accepted format.+                         return pnextp+  _ <- word8 09+  tlen <- do tlenp <- DABL.takeTill (== 09)+             -- Parse TLEN field of the alignment section.+             case (tlenp =~ [re|[-]?[0-9]*|]) of+               False -> fail $ show SAM_V1_6_Error_Alignment_TLEN_Incorrect_Format +               True  -> -- TLEN is in the accepted format.+                        return tlenp+  _ <- word8 09+  seq <- do seqp <- DABL.takeTill (== 09)+            -- Parse SEQ field of the alignment section.+            case (seqp =~ [re|\*|[A-Za-z=.]+|]) of+              False -> fail $ show SAM_V1_6_Error_Alignment_SEQ_Incorrect_Format +              True  -> -- SEQ is in the accepted format.+                       return seqp+  _ <- word8 09+  qual <- do qualp <- DABL.takeTill (== 09)+             -- Parse QUAL field of the alignment section.+             case (qualp =~ [re|[!-~]+|]) of+               False -> fail $ show SAM_V1_6_Error_Alignment_QUAL_Incorrect_Format+               True  -> -- QUAL is in the accepted format.+                        return qualp+  _ <- word8 09+  -- This parser assumes that the AOPT tag always appears first,+  -- followed by IOPT, FOPT, ZOPT, HOPT, and BOPT, if they exist,+  -- in that order.+  aopt <- maybeOption parse_SAM_V1_6_Alignment_AOPT+  _    <- word8 09+  iopt <- maybeOption parse_SAM_V1_6_Alignment_IOPT+  _    <- word8 09+  fopt <- maybeOption parse_SAM_V1_6_Alignment_FOPT+  _    <- word8 09+  zopt <- maybeOption parse_SAM_V1_6_Alignment_ZOPT+  _    <- word8 09+  hopt <- maybeOption parse_SAM_V1_6_Alignment_HOPT+  _    <- word8 09+  bopt <- maybeOption parse_SAM_V1_6_Alignment_BOPT+  -- Return the parsed SAM_V1_6.+  return SAM_V1_6_Alignment { sam_v1_6_alignment_qname  = qname+                            , sam_v1_6_alignment_flag   = case (DBC8.readInt flag) of+                                                            Nothing          -> (-1)+                                                            Just (flagint,_) -> flagint+                            , sam_v1_6_alignment_rname = rname+                            , sam_v1_6_alignment_pos   = case (DBC8.readInteger pos) of+                                                           Nothing             -> 0+                                                           Just (posinteger,_) -> posinteger+                            , sam_v1_6_alignment_mapq  = case (DBC8.readInt mapq) of+                                                           Nothing          -> 255+                                                           Just (mapqint,_) -> mapqint+                            , sam_v1_6_alignment_cigar = cigar+                            , sam_v1_6_alignment_rnext = rnext+                            , sam_v1_6_alignment_pnext = case (DBC8.readInteger pnext) of+                                                           Nothing               -> 0+                                                           Just (pnextinteger,_) -> pnextinteger+                            , sam_v1_6_alignment_tlen  = case (DBC8.readInteger tlen) of+                                                           Nothing              -> 0+                                                           Just (tleninteger,_) -> tleninteger+                            , sam_v1_6_alignment_seq   = seq+                            , sam_v1_6_alignment_qual  = qual+                            , sam_v1_6_alignment_aopt  = aopt+                            , sam_v1_6_alignment_iopt  = iopt+                            , sam_v1_6_alignment_fopt  = fopt+                            , sam_v1_6_alignment_zopt  = zopt+                            , sam_v1_6_alignment_hopt  = hopt+                            , sam_v1_6_alignment_bopt  = bopt+                            }
+ src/Data/SAM/Version1_6/Read/Parser/Alignment/FOPT.hs view
@@ -0,0 +1,80 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Alignment.FOPT+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Alignment.FOPT ( -- * SAM_V1_6 parser - alignment section - fopt field +                                                        parse_SAM_V1_6_Alignment_FOPT+                                                      ) where++import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString.Char8             as DBC8+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the optional fopt field of alignment section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_Alignment_FOPT :: Parser Float+parse_SAM_V1_6_Alignment_FOPT = do+  _ <- do alignmentfoptfieldtagp <- DABL.takeTill (== 58)+          -- Parse FOPT tag of the alignment section.+          case (alignmentfoptfieldtagp =~ [re|/[A-Za-z][A-Za-z0-9]/|]) of+            False -> fail $ show SAM_V1_6_Error_Alignment_FOPT_Tag_Incorrect_Format+            True  -> -- FOPT tag is in the accepted format. +                     return alignmentfoptfieldtagp+  _ <- word8 58+  _ <- do alignmentfoptfieldtypep <- DABL.takeTill (== 58)+          -- Parse FOPT type of the alignment section.+          case (alignmentfoptfieldtypep =~ [re|[f]|]) of+            False -> fail $ show SAM_V1_6_Error_Alignment_FOPT_Type_Incorrect_Format+            True  -> -- FOPT type is in the accepted format.+                     return alignmentfoptfieldtypep+  _ <- word8 58+  alignmentfoptfieldvalue <- do alignmentfoptfieldvaluep <- DABL.takeTill (== 09)+                                -- Parse FOPT value of the alignment section.+                                case (alignmentfoptfieldvaluep =~ [re|[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?|]) of+                                  False -> fail $ show SAM_V1_6_Error_Alignment_FOPT_Value_Incorrect_Format+                                  True  -> -- FOPT value is in the accepted format.+                                           case (DBC8.readInteger alignmentfoptfieldvaluep) of+                                             Nothing                                 -> return (-1)+                                             Just (alignmentfoptfieldvalueinteger,_) -> return $ (fromInteger alignmentfoptfieldvalueinteger :: Float)+  return alignmentfoptfieldvalue
+ src/Data/SAM/Version1_6/Read/Parser/Alignment/HOPT.hs view
@@ -0,0 +1,80 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Alignment.HOPT+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Alignment.HOPT ( -- * SAM_V1_6 parser - alignment section - hopt field +                                                        parse_SAM_V1_6_Alignment_HOPT+                                                      ) where++import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB+import           Data.Sequence                     as DSeq+import           Data.Word+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the optional hopt field of alignment section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_Alignment_HOPT :: Parser (Seq Word8)+parse_SAM_V1_6_Alignment_HOPT = do+  _ <- do alignmenthoptfieldtagp <- DABL.takeTill (== 58)+          -- Parse HOPT tag of the alignment section.+          case (alignmenthoptfieldtagp =~ [re|/[A-Za-z][A-Za-z0-9]/|]) of+            False -> fail $ show SAM_V1_6_Error_Alignment_HOPT_Tag_Incorrect_Format+            True  -> -- HOPT tag is in the accepted format. +                     return alignmenthoptfieldtagp+  _ <- word8 58+  _ <- do alignmenthoptfieldtypep <- DABL.takeTill (== 58)+          -- Parse HOPT type of the alignment section.+          case (alignmenthoptfieldtypep =~ [re|[H]|]) of+            False -> fail $ show SAM_V1_6_Error_Alignment_HOPT_Type_Incorrect_Format+            True  -> -- HOPT type is in the accepted format.+                     return alignmenthoptfieldtypep+  _ <- word8 58+  alignmenthoptfieldvalue <- do alignmenthoptfieldvaluep <- DABL.takeTill (== 09)+                                -- Parse HOPT value of the alignment section.+                                case (alignmenthoptfieldvaluep =~ [re|([0-9A-F][0-9A-F])*|]) of+                                  False -> fail $ show SAM_V1_6_Error_Alignment_HOPT_Value_Incorrect_Format+                                  True  -> -- HOPT value is in the accepted format.+                                           return $ DSeq.fromList $ DB.unpack alignmenthoptfieldvaluep+  return alignmenthoptfieldvalue
+ src/Data/SAM/Version1_6/Read/Parser/Alignment/IOPT.hs view
@@ -0,0 +1,80 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Alignment.IOPT+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Alignment.IOPT ( -- * SAM_V1_6 parser - alignment section - iopt field +                                                        parse_SAM_V1_6_Alignment_IOPT+                                                      ) where++import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString.Char8             as DBC8+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the optional iopt field of alignment section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_Alignment_IOPT :: Parser Integer+parse_SAM_V1_6_Alignment_IOPT = do+  _ <- do alignmentioptfieldtagp <- DABL.takeTill (== 58)+          -- Parse IOPT tag of the alignment section.+          case (alignmentioptfieldtagp =~ [re|/[A-Za-z][A-Za-z0-9]/|]) of+            False -> fail $ show SAM_V1_6_Error_Alignment_IOPT_Tag_Incorrect_Format+            True  -> -- IOPT tag is in the accepted format. +                     return alignmentioptfieldtagp+  _ <- word8 58+  _ <- do alignmentioptfieldtypep <- DABL.takeTill (== 58)+          -- Parse IOPT type of the alignment section.+          case (alignmentioptfieldtypep =~ [re|[i]|]) of+            False -> fail $ show SAM_V1_6_Error_Alignment_IOPT_Type_Incorrect_Format+            True  -> -- IOPT type is in the accepted format.+                     return alignmentioptfieldtypep+  _ <- word8 58+  alignmentioptfieldvalue <- do alignmentioptfieldvaluep <- DABL.takeTill (== 09)+                                -- Parse IOPT value of the alignment section.+                                case (alignmentioptfieldvaluep =~ [re|[-+]?[0-9]+|]) of+                                  False -> fail $ show SAM_V1_6_Error_Alignment_IOPT_Value_Incorrect_Format+                                  True  -> -- IOPT value is in the accepted format.+                                           case (DBC8.readInteger alignmentioptfieldvaluep) of+                                             Nothing                                 -> return (-1)+                                             Just (alignmentioptfieldvalueinteger,_) -> return alignmentioptfieldvalueinteger+  return alignmentioptfieldvalue
+ src/Data/SAM/Version1_6/Read/Parser/Alignment/ZOPT.hs view
@@ -0,0 +1,78 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# Language QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Alignment.ZOPT+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Alignment.ZOPT ( -- * SAM_V1_6 parser - alignment section - zopt field +                                                        parse_SAM_V1_6_Alignment_ZOPT+                                                      ) where++import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the optional zopt field of alignment section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_Alignment_ZOPT :: Parser DB.ByteString+parse_SAM_V1_6_Alignment_ZOPT = do+  _ <- do alignmentzoptfieldtagp <- DABL.takeTill (== 58)+          -- Parse ZOPT tag of the alignment section.+          case (alignmentzoptfieldtagp =~ [re|/[A-Za-z][A-Za-z0-9]/|]) of+            False -> fail $ show SAM_V1_6_Error_Alignment_ZOPT_Tag_Incorrect_Format+            True  -> -- ZOPT tag is in the accepted format. +                     return alignmentzoptfieldtagp+  _ <- word8 58+  _ <- do alignmentzoptfieldtypep <- DABL.takeTill (== 58)+          -- Parse ZOPT type of the alignment section.+          case (alignmentzoptfieldtypep =~ [re|[Z]|]) of+            False -> fail $ show SAM_V1_6_Error_Alignment_ZOPT_Type_Incorrect_Format+            True  -> -- ZOPT type is in the accepted format.+                     return alignmentzoptfieldtypep+  _ <- word8 58+  alignmentzoptfieldvalue <- do alignmentzoptfieldvaluep <- DABL.takeTill (== 09)+                                -- Parse ZOPT value of the alignment section.+                                case (alignmentzoptfieldvaluep =~ [re|[ !-~]*|]) of+                                  False -> fail $ show SAM_V1_6_Error_Alignment_ZOPT_Value_Incorrect_Format+                                  True  -> -- ZOPT value is in the accepted format.+                                           return alignmentzoptfieldvaluep+  return alignmentzoptfieldvalue
+ src/Data/SAM/Version1_6/Read/Parser/Header/CO/Base.hs view
@@ -0,0 +1,71 @@+{-# LANGUAGE DeriveDataTypeable          #-}+{-# LANGUAGE DeriveGeneric               #-}+{-# LANGUAGE FlexibleContexts            #-}+{-# LANGUAGE FlexibleInstances           #-}+{-# LANGUAGE MultiParamTypeClasses       #-}+{-# LANGUAGE OverloadedLists             #-}+{-# LANGUAGE OverloadedStrings           #-}+{-# LANGUAGE MultiWayIf                  #-}+{-# LANGUAGE PackageImports              #-}+{-# LANGUAGE RecordWildCards             #-}+{-# LANGUAGE ScopedTypeVariables         #-}+{-# LANGUAGE TemplateHaskell             #-}+{-# LANGUAGE TypeFamilies                #-}+{-# LANGUAGE QuasiQuotes                 #-}+{-# OPTIONS_GHC -fno-warn-name-shadowing #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.CO.Base+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.CO.Base ( -- * SAM_V1_6 parser - header section (One-line text comment)+                                                        parse_SAM_V1_6_One_Line_Comment+                                                      ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import Data.Attoparsec.ByteString.Char8  as DABC8+import Data.Attoparsec.ByteString.Lazy   as DABL+import Text.Regex.PCRE.Heavy++-- | @"SAM_V1_6_One_Line_Comment"@ parser.+--+-- Defines a parser for @CO tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_One_Line_Comment :: Parser SAM_V1_6_One_Line_Comment+parse_SAM_V1_6_One_Line_Comment = do+  _         <- do coheaderp <- DABL.takeTill (== 09)+                  -- Parse @PG tag of the header section.+                  case (coheaderp =~ [re|[@][C][O]|]) of+                    False -> fail $ show SAM_V1_6_Error_One_Line_Comment_Tag_Incorrect_Format+                    True  -> -- @CO tag is in the accepted format.+                             return coheaderp+  _         <- word8 09+  value     <- DABL.takeTill (\x -> x == 13 || x == 10)+  return SAM_V1_6_One_Line_Comment { sam_v1_6_one_line_comment_value = value+                                   }
+ src/Data/SAM/Version1_6/Read/Parser/Header/HD/Base.hs view
@@ -0,0 +1,89 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.HD.Base+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.HD.Base ( -- * SAM_V1_6 parser - header section (File-level metadata)+                                                        parse_SAM_V1_6_File_Level_Metadata+                                                      ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error+import Data.SAM.Version1_6.Read.Parser.Header.HD.VN+import Data.SAM.Version1_6.Read.Parser.Header.HD.SO+import Data.SAM.Version1_6.Read.Parser.Header.HD.GO+import Data.SAM.Version1_6.Read.Parser.Header.HD.SS++import Data.Attoparsec.ByteString.Lazy   as DABL+import Text.Regex.PCRE.Heavy++-- | Make a parser optional, return Nothing if there is no match.+maybeOption :: Parser a+            -> Parser (Maybe a)+maybeOption p = option Nothing (Just <$> p)++-- | @"SAM_V1_6_File_Level_Metadata"@ parser.+--+-- Defines a parser for @HD tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_File_Level_Metadata :: Parser SAM_V1_6_File_Level_Metadata+parse_SAM_V1_6_File_Level_Metadata = do+  _         <- do hdheaderp <- DABL.takeTill (== 09)+                  -- Parse @HD tag of the header section.+                  case (hdheaderp =~ [re|[@][H][D]|]) of+                    False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Tag_Incorrect_Format+                    True  -> -- @HD tag is in the accepted format.+                             return hdheaderp+  _         <- word8 09+  -- This parser assumes that the VN tag always appears first, followed by+  -- SO, GO and SS tags, if they exist, in that order.+  vn <- parse_SAM_V1_6_File_Level_Metadata_VN+  _  <- word8 09+  so <- maybeOption parse_SAM_V1_6_File_Level_Metadata_SO+  _  <- word8 09+  go <- maybeOption parse_SAM_V1_6_File_Level_Metadata_GO+  _  <- word8 09+  ss <- maybeOption parse_SAM_V1_6_File_Level_Metadata_SS+  return SAM_V1_6_File_Level_Metadata { sam_v1_6_file_level_metadata_format_version     = vn+                                      , sam_v1_6_file_level_metadata_sorting_order      = so+                                      , sam_v1_6_file_level_metadata_alignment_grouping = go+                                      , sam_v1_6_file_level_metadata_subsorting_order   = ss+                                      }
+ src/Data/SAM/Version1_6/Read/Parser/Header/HD/GO.hs view
@@ -0,0 +1,75 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.HD.GO+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.HD.GO ( -- * SAM_V1_6 parser - header section (File-level metadata) - GO tag+                                                      parse_SAM_V1_6_File_Level_Metadata_GO+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the GO tag of the @HD tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_File_Level_Metadata_GO :: Parser SAM_V1_6_File_Level_Metadata_Alignment_Grouping+parse_SAM_V1_6_File_Level_Metadata_GO = do+  hdheaderalignmentgroupingtag <- do hdheaderalignmentgroupingtagp <- DABL.takeTill (== 58)+                                     -- Parse GO tag of the header section.+                                     case (hdheaderalignmentgroupingtagp =~ [re|[G][O]|]) of+                                       False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Grouping_Of_Alignments_Tag_Incorrect_Format+                                       True  -> -- GO tag is in the accepted format.+                                                return hdheaderalignmentgroupingtagp+  _ <- word8 58+  hdheaderalignmentgroupingvalue <- do hdheaderalignmentgroupingvaluep <- DABL.takeTill (== 09)+                                       -- Parse GO value of the header section.+                                       case (hdheaderalignmentgroupingvaluep =~ [re|[n][o][n][e]|[q][u][e][r][y]|[r][e][f][e][r][e][n][c][e]|]) of+                                         False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Grouping_Of_Alignments_Invalid_Value+                                         True  -> -- GO value is in the accepted format.+                                                  return hdheaderalignmentgroupingvaluep+  return SAM_V1_6_File_Level_Metadata_Alignment_Grouping { sam_v1_6_file_level_metadata_alignment_grouping_tag   = DSeq.fromList $ DB.unpack hdheaderalignmentgroupingtag+                                                         , sam_v1_6_file_level_metadata_alignment_grouping_value = hdheaderalignmentgroupingvalue+                                                         }
+ src/Data/SAM/Version1_6/Read/Parser/Header/HD/SO.hs view
@@ -0,0 +1,75 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.HD.SO+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.HD.SO ( -- * SAM_V1_6 parser - header section (File-level metadata) - SO tag+                                                      parse_SAM_V1_6_File_Level_Metadata_SO+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the SO tag of the @HD tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_File_Level_Metadata_SO :: Parser SAM_V1_6_File_Level_Metadata_Sorting_Order+parse_SAM_V1_6_File_Level_Metadata_SO = do+  hdheadersortingordertag <- do hdheadersortingordertagp <- DABL.takeTill (== 58)+                                -- Parse SO tag of the header section.+                                case (hdheadersortingordertagp =~ [re|[S][O]|]) of+                                  False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Sorting_Order_Tag_Incorrect_Format+                                  True  -> -- SO tag is in the accepted format.+                                           return hdheadersortingordertagp+  _ <- word8 58+  hdheadersortingordervalue <- do hdheadersortingordervaluep <- DABL.takeTill (== 09)+                                  -- Parse SO value of the header section.+                                  case (hdheadersortingordervaluep =~ [re|[u][n][k][n][o][w][n]|[u][n][s][o][r][t][e][d]|[q][u][e][r][y][n][a][m][e]|[c][o][o][r][d][i][n][a][t][e]|]) of+                                    False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Sorting_Order_Invalid_Value+                                    True  -> -- SO value is in the accepted format.+                                             return hdheadersortingordervaluep  +  return SAM_V1_6_File_Level_Metadata_Sorting_Order { sam_v1_6_file_level_metadata_sorting_order_tag   = DSeq.fromList $ DB.unpack hdheadersortingordertag+                                                    , sam_v1_6_file_level_metadata_sorting_order_value = hdheadersortingordervalue+                                                    }
+ src/Data/SAM/Version1_6/Read/Parser/Header/HD/SS.hs view
@@ -0,0 +1,75 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.HD.SS+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.HD.SS ( -- * SAM_V1_6 parser - header section (File-level metadata) - SS tag+                                                      parse_SAM_V1_6_File_Level_Metadata_SS+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the SS tag of the @HD tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_File_Level_Metadata_SS :: Parser SAM_V1_6_File_Level_Metadata_SubSorting_Order+parse_SAM_V1_6_File_Level_Metadata_SS = do+  hdheadersubsortingordertag <- do hdheadersubsortingordertagp <- DABL.takeTill (== 58)+                                   -- Parse SS tag of the header section.+                                   case (hdheadersubsortingordertagp =~ [re|[S][S]|]) of+                                     False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Subsorting_Order_Tag_Incorrect_Format+                                     True  -> -- SS tag is in the accepted format.+                                              return hdheadersubsortingordertagp+  _ <- word8 58+  hdheadersubsortingordervalue <- do hdheadersubsortingordervaluep <- DABL.takeTill (== 09)+                                     -- Parse SS value of the header section.+                                     case (hdheadersubsortingordervaluep =~ [re|(coordinate|queryname|unsorted)(:[A-Za-z0-9_-]+)+|]) of+                                       False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Subsorting_Order_Incorrect_Format +                                       True  -> -- SS value is in the accepted format.+                                                return hdheadersubsortingordervaluep +  return SAM_V1_6_File_Level_Metadata_SubSorting_Order { sam_v1_6_file_level_metadata_subsorting_order_tag   = DSeq.fromList $ DB.unpack hdheadersubsortingordertag+                                                       , sam_v1_6_file_level_metadata_subsorting_order_value = hdheadersubsortingordervalue+                                                       }
+ src/Data/SAM/Version1_6/Read/Parser/Header/HD/VN.hs view
@@ -0,0 +1,75 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.HD.VN+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.HD.VN ( -- * SAM_V1_6 parser - header section (File-level metadata) - VN tag+                                                      parse_SAM_V1_6_File_Level_Metadata_VN+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the VN tag of the @HD tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_File_Level_Metadata_VN :: Parser SAM_V1_6_File_Level_Metadata_Format_Version+parse_SAM_V1_6_File_Level_Metadata_VN = do+  hdheaderversiontag <- do hdheaderversiontagp <- DABL.takeTill (== 58)+                           -- Parse VN tag of the header section.+                           case (hdheaderversiontagp =~ [re|[V][N]|]) of+                             False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Format_Version_Tag_Incorrect_Format+                             True  -> -- VN tag is in the accepted format. +                                      return hdheaderversiontagp+  _ <- word8 58+  hdheaderversionvalue <- do hdheaderversionvaluep <- DABL.takeTill (== 09)+                             -- Parse VN value of the header section.+                             case (hdheaderversionvaluep =~ [re|/^[0-9]+\.[0-9]+$/.|]) of+                               False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Format_Version_Value_Incorrect_Format+                               True  -> -- VN value is in the accepted format.+                                        return hdheaderversionvaluep  +  return SAM_V1_6_File_Level_Metadata_Format_Version { sam_v1_6_file_level_metadata_format_version_tag   = DSeq.fromList $ DB.unpack hdheaderversiontag+                                                     , sam_v1_6_file_level_metadata_format_version_value = hdheaderversionvalue+                                                     }
+ src/Data/SAM/Version1_6/Read/Parser/Header/PG/Base.hs view
@@ -0,0 +1,99 @@+{-# LANGUAGE DeriveDataTypeable          #-}+{-# LANGUAGE DeriveGeneric               #-}+{-# LANGUAGE FlexibleContexts            #-}+{-# LANGUAGE FlexibleInstances           #-}+{-# LANGUAGE MultiParamTypeClasses       #-}+{-# LANGUAGE OverloadedLists             #-}+{-# LANGUAGE OverloadedStrings           #-}+{-# LANGUAGE MultiWayIf                  #-}+{-# LANGUAGE PackageImports              #-}+{-# LANGUAGE RecordWildCards             #-}+{-# LANGUAGE ScopedTypeVariables         #-}+{-# LANGUAGE TemplateHaskell             #-}+{-# LANGUAGE TypeFamilies                #-}+{-# LANGUAGE QuasiQuotes                 #-}+{-# OPTIONS_GHC -fno-warn-name-shadowing #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.PG.Base+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.PG.Base ( -- * SAM_V1_6 parser - header section (Program)+                                                        parse_SAM_V1_6_Program+                                                      ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error+import Data.SAM.Version1_6.Read.Parser.Header.PG.ID+import Data.SAM.Version1_6.Read.Parser.Header.PG.PN+import Data.SAM.Version1_6.Read.Parser.Header.PG.CL+import Data.SAM.Version1_6.Read.Parser.Header.PG.PP+import Data.SAM.Version1_6.Read.Parser.Header.PG.DS+import Data.SAM.Version1_6.Read.Parser.Header.PG.VN++import Data.Attoparsec.ByteString.Lazy   as DABL+import Text.Regex.PCRE.Heavy++-- | Make a parser optional, return Nothing if there is no match.+maybeOption :: Parser a+            -> Parser (Maybe a)+maybeOption p = option Nothing (Just <$> p)++-- | @"SAM_V1_6_Program"@ parser.+--+-- Defines a parser for @PG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_Program :: Parser SAM_V1_6_Program+parse_SAM_V1_6_Program = do+  _         <- do pgheaderp <- DABL.takeTill (== 09)+                  -- Parse @PG tag of the header section.+                  case (pgheaderp =~ [re|[@][P][G]|]) of+                    False -> fail $ show SAM_V1_6_Error_Program_Tag_Incorrect_Format +                    True  -> -- @PG tag is in the accepted format.+                             return pgheaderp+  _         <- word8 09+  -- This parser assumes that the ID tag always appears first, followed by+  -- the PN, CL, PP,+  -- DS and VN tags if they exist, in that order.+  id <- parse_SAM_V1_6_SAM_V1_6_Program_ID+  _  <- word8 09+  pn <- maybeOption parse_SAM_V1_6_SAM_V1_6_Program_PN+  _  <- word8 09+  cl <- maybeOption parse_SAM_V1_6_SAM_V1_6_Program_CL+  _  <- word8 09+  pp <- maybeOption parse_SAM_V1_6_SAM_V1_6_Program_PP+  _  <- word8 09+  ds <- maybeOption parse_SAM_V1_6_SAM_V1_6_Program_DS+  _  <- word8 09+  vn <- maybeOption parse_SAM_V1_6_SAM_V1_6_Program_VN+  return SAM_V1_6_Program { sam_v1_6_program_record_identifier = id+                          , sam_v1_6_program_name              = pn+                          , sam_v1_6_program_command_line      = cl+                          , sam_v1_6_program_previous_pg_id    = pp+                          , sam_v1_6_program_description       = ds+                          , sam_v1_6_program_version           = vn+                          }
+ src/Data/SAM/Version1_6/Read/Parser/Header/PG/CL.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.PG.CL+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.PG.CL ( -- * SAM_V1_6 parser - header section (Program) - CL tag+                                                      parse_SAM_V1_6_SAM_V1_6_Program_CL+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the CL tag of the @PG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Program_CL :: Parser SAM_V1_6_Program_Command_Line+parse_SAM_V1_6_SAM_V1_6_Program_CL = do+  pgheadercommandlinetag <- do pgheadercommandlinetagp <- DABL.takeTill (== 58)+                               -- Parse CL tag of the header section.+                               case (pgheadercommandlinetagp =~ [re|[C][L]|]) of+                                 False -> fail $ show SAM_V1_6_Error_Program_Command_Line_Incorrect_Format +                                 True  -> -- CL tag is in the accepted format. +                                          return pgheadercommandlinetagp+  _ <- word8 58+  pgheadercommandlinevalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Program_Command_Line { sam_v1_6_program_command_line_tag   = DSeq.fromList $ DB.unpack pgheadercommandlinetag+                                       , sam_v1_6_program_command_line_value = pgheadercommandlinevalue+                                       }
+ src/Data/SAM/Version1_6/Read/Parser/Header/PG/DS.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.PG.DS+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.PG.DS ( -- * SAM_V1_6 parser - header section (Program) - DS tag+                                                      parse_SAM_V1_6_SAM_V1_6_Program_DS+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the DS tag of the @PG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Program_DS :: Parser SAM_V1_6_Program_Description+parse_SAM_V1_6_SAM_V1_6_Program_DS = do+  pgheaderdescriptiontag <- do pgheaderdescriptiontagp <- DABL.takeTill (== 58)+                               -- Parse DS tag of the header section.+                               case (pgheaderdescriptiontagp =~ [re|[D][S]|]) of+                                 False -> fail $ show SAM_V1_6_Error_Program_Description_Incorrect_Format +                                 True  -> -- DS tag is in the accepted format. +                                          return pgheaderdescriptiontagp+  _ <- word8 58+  pgheaderdescriptionvalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Program_Description { sam_v1_6_program_description_tag   = DSeq.fromList $ DB.unpack pgheaderdescriptiontag+                                      , sam_v1_6_program_description_value = pgheaderdescriptionvalue+                                      }
+ src/Data/SAM/Version1_6/Read/Parser/Header/PG/ID.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.PG.ID+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.PG.ID ( -- * SAM_V1_6 parser - header section (Program) - ID tag+                                                      parse_SAM_V1_6_SAM_V1_6_Program_ID+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the ID tag of the @PG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Program_ID :: Parser SAM_V1_6_Program_Record_Identifier+parse_SAM_V1_6_SAM_V1_6_Program_ID = do+  pgheaderidentifiertag <- do pgheaderidentifiertagp <- DABL.takeTill (== 58)+                              -- Parse ID tag of the header section.+                              case (pgheaderidentifiertagp =~ [re|[I][D]|]) of+                                False -> fail $ show SAM_V1_6_Error_Program_Identifier_Incorrect_Format +                                True  -> -- ID tag is in the accepted format. +                                         return pgheaderidentifiertagp+  _ <- word8 58+  pgheaderidentifiervalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Program_Record_Identifier { sam_v1_6_program_record_identifier_tag   = DSeq.fromList $ DB.unpack pgheaderidentifiertag+                                            , sam_v1_6_program_record_identifier_value = pgheaderidentifiervalue+                                            }
+ src/Data/SAM/Version1_6/Read/Parser/Header/PG/PN.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.PG.PN+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.PG.PN ( -- * SAM_V1_6 parser - header section (Program) - PN tag+                                                      parse_SAM_V1_6_SAM_V1_6_Program_PN+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the PN tag of the @PG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Program_PN :: Parser SAM_V1_6_Program_Name+parse_SAM_V1_6_SAM_V1_6_Program_PN = do+  pgheadernametag <- do pgheadernametagp <- DABL.takeTill (== 58)+                        -- Parse PN tag of the header section.+                        case (pgheadernametagp =~ [re|[P][N]|]) of+                          False -> fail $ show SAM_V1_6_Error_Program_Name_Incorrect_Format +                          True  -> -- PN tag is in the accepted format. +                                   return pgheadernametagp+  _ <- word8 58+  pgheadernamevalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Program_Name { sam_v1_6_program_name_tag   = DSeq.fromList $ DB.unpack pgheadernametag+                               , sam_v1_6_program_name_value = pgheadernamevalue+                               }
+ src/Data/SAM/Version1_6/Read/Parser/Header/PG/PP.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.PG.PP+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.PG.PP ( -- * SAM_V1_6 parser - header section (Program) - PP tag+                                                      parse_SAM_V1_6_SAM_V1_6_Program_PP+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the PP tag of the @PG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Program_PP :: Parser SAM_V1_6_Program_Previous_PG_ID+parse_SAM_V1_6_SAM_V1_6_Program_PP = do+  pgheaderpreviouspgidtag <- do pgheaderpreviouspgidtagp <- DABL.takeTill (== 58)+                                -- Parse PP tag of the header section.+                                case (pgheaderpreviouspgidtagp =~ [re|[P][P]|]) of+                                  False -> fail $ show SAM_V1_6_Error_Program_Previous_PG_ID_Incorrect_Format +                                  True  -> -- PP tag is in the accepted format. +                                           return pgheaderpreviouspgidtagp+  _ <- word8 58+  pgheaderpreviouspgidvalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Program_Previous_PG_ID { sam_v1_6_program_previous_pg_id_tag   = DSeq.fromList $ DB.unpack pgheaderpreviouspgidtag+                                         , sam_v1_6_program_previous_pg_id_value = pgheaderpreviouspgidvalue+                                         }
+ src/Data/SAM/Version1_6/Read/Parser/Header/PG/VN.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.PG.VN+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.PG.VN ( -- * SAM_V1_6 parser - header section (Program) - VN tag+                                                      parse_SAM_V1_6_SAM_V1_6_Program_VN+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the VN tag of the @PG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Program_VN :: Parser SAM_V1_6_Program_Version+parse_SAM_V1_6_SAM_V1_6_Program_VN = do+  pgheaderversiontag <- do pgheaderversiontagp <- DABL.takeTill (== 58)+                           -- Parse VN tag of the header section.+                           case (pgheaderversiontagp =~ [re|[V][N]|]) of+                             False -> fail $ show SAM_V1_6_Error_Program_Version_Incorrect_Format +                             True  -> -- VN tag is in the accepted format. +                                      return pgheaderversiontagp+  _ <- word8 58+  pgheaderversionvalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Program_Version { sam_v1_6_program_version_tag   = DSeq.fromList $ DB.unpack pgheaderversiontag+                                  , sam_v1_6_program_version_value = pgheaderversionvalue+                                  }
+ src/Data/SAM/Version1_6/Read/Parser/Header/RG/BC.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.RG.BC+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.RG.BC ( -- * SAM_V1_6 parser - header section (Read group) - BC tag+                                                      parse_SAM_V1_6_SAM_V1_6_Read_Group_BC+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the BC tag of the @RG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Read_Group_BC :: Parser SAM_V1_6_Read_Group_Barcode_Sequence +parse_SAM_V1_6_SAM_V1_6_Read_Group_BC = do+  rgheaderbarcodesequencetag <- do rgheaderbarcodesequencetagp <- DABL.takeTill (== 58)+                                   -- Parse BC tag of the header section.+                                   case (rgheaderbarcodesequencetagp =~ [re|[B][C]|]) of+                                     False -> fail $ show SAM_V1_6_Error_Read_Group_Barcode_Sequence_Incorrect_Format +                                     True  -> -- BC tag is in the accepted format. +                                              return rgheaderbarcodesequencetagp+  _ <- word8 58+  rgheaderbarcodesequencevalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Read_Group_Barcode_Sequence { sam_v1_6_read_group_barcode_sequence_tag   = DSeq.fromList $ DB.unpack rgheaderbarcodesequencetag+                                              , sam_v1_6_read_group_barcode_sequence_value = rgheaderbarcodesequencevalue+                                              }
+ src/Data/SAM/Version1_6/Read/Parser/Header/RG/Base.hs view
@@ -0,0 +1,131 @@+{-# LANGUAGE DeriveDataTypeable          #-}+{-# LANGUAGE DeriveGeneric               #-}+{-# LANGUAGE FlexibleContexts            #-}+{-# LANGUAGE FlexibleInstances           #-}+{-# LANGUAGE MultiParamTypeClasses       #-}+{-# LANGUAGE OverloadedLists             #-}+{-# LANGUAGE OverloadedStrings           #-}+{-# LANGUAGE MultiWayIf                  #-}+{-# LANGUAGE PackageImports              #-}+{-# LANGUAGE RecordWildCards             #-}+{-# LANGUAGE ScopedTypeVariables         #-}+{-# LANGUAGE TemplateHaskell             #-}+{-# LANGUAGE TypeFamilies                #-}+{-# LANGUAGE QuasiQuotes                 #-}+{-# OPTIONS_GHC -fno-warn-name-shadowing #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.RG.Base+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.RG.Base ( -- * SAM_V1_6 parser - header section (Read group)+                                                        parse_SAM_V1_6_Read_Group+                                                      ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error+import Data.SAM.Version1_6.Read.Parser.Header.RG.ID+import Data.SAM.Version1_6.Read.Parser.Header.RG.BC+import Data.SAM.Version1_6.Read.Parser.Header.RG.CN+import Data.SAM.Version1_6.Read.Parser.Header.RG.DS+import Data.SAM.Version1_6.Read.Parser.Header.RG.DT+import Data.SAM.Version1_6.Read.Parser.Header.RG.FO+import Data.SAM.Version1_6.Read.Parser.Header.RG.KS+import Data.SAM.Version1_6.Read.Parser.Header.RG.LB+import Data.SAM.Version1_6.Read.Parser.Header.RG.PG+import Data.SAM.Version1_6.Read.Parser.Header.RG.PI+import Data.SAM.Version1_6.Read.Parser.Header.RG.PL+import Data.SAM.Version1_6.Read.Parser.Header.RG.PM+import Data.SAM.Version1_6.Read.Parser.Header.RG.PU+import Data.SAM.Version1_6.Read.Parser.Header.RG.SM++import Data.Attoparsec.ByteString.Lazy   as DABL+import Text.Regex.PCRE.Heavy++-- | Make a parser optional, return Nothing if there is no match.+maybeOption :: Parser a+            -> Parser (Maybe a)+maybeOption p = option Nothing (Just <$> p)++-- | @"SAM_V1_6_Read_Group"@ parser.+--+-- Defines a parser for @RG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_Read_Group :: Parser SAM_V1_6_Read_Group+parse_SAM_V1_6_Read_Group = do+  _         <- do rgheaderp <- DABL.takeTill (== 09)+                  -- Parse @RG tag of the header section.+                  case (rgheaderp =~ [re|[@][R][G]|]) of+                    False -> fail $ show SAM_V1_6_Error_Read_Group_Tag_Incorrect_Format+                    True  -> -- @RG tag is in the accepted format.+                             return rgheaderp+  _         <- word8 09+  -- This parser assumes that the ID tag always appears first, followed by+  -- the BC, CN, DS, DT, FO, KS, LB, PG, PI, PL,+  -- PM, PU and SM tags if they exist, in that order.+  id <- parse_SAM_V1_6_SAM_V1_6_Read_Group_ID+  _  <- word8 09+  bc <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_BC+  _  <- word8 09+  cn <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_CN+  _  <- word8 09+  ds <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_DS+  _  <- word8 09+  dt <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_DT+  _  <- word8 09+  fo <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_FO+  _  <- word8 09+  ks <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_KS+  _  <- word8 09+  lb <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_LB+  _  <- word8 09+  pg <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_PG+  _  <- word8 09+  pi <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_PI+  _  <- word8 09+  pl <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_PL+  _  <- word8 09+  pm <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_PM+  _  <- word8 09+  pu <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_PU+  _  <- word8 09+  sm <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_SM+  return SAM_V1_6_Read_Group { sam_v1_6_read_group_identifer                    = id+                             , sam_v1_6_read_group_barcode_sequence             = bc+                             , sam_v1_6_read_group_sequencing_center            = cn+                             , sam_v1_6_read_group_description                  = ds+                             , sam_v1_6_read_group_run_date                     = dt+                             , sam_v1_6_read_group_flow_order                   = fo+                             , sam_v1_6_read_group_key_sequence                 = ks+                             , sam_v1_6_read_group_library                      = lb+                             , sam_v1_6_read_group_programs                     = pg+                             , sam_v1_6_read_group_predicted_median_insert_size = pi+                             , sam_v1_6_read_group_platform                     = pl+                             , sam_v1_6_read_group_platform_model               = pm+                             , sam_v1_6_read_group_platform_unit                = pu+                             , sam_v1_6_read_group_sample                       = sm+                             }
+ src/Data/SAM/Version1_6/Read/Parser/Header/RG/CN.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.RG.CN+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.RG.CN ( -- * SAM_V1_6 parser - header section (Read group) - CN tag+                                                      parse_SAM_V1_6_SAM_V1_6_Read_Group_CN+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the CN tag of the @RG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Read_Group_CN :: Parser SAM_V1_6_Read_Group_Sequencing_Center +parse_SAM_V1_6_SAM_V1_6_Read_Group_CN = do+  rgheadersequencingcentertag <- do rgheadersequencingcentertagp <- DABL.takeTill (== 58)+                                    -- Parse CN tag of the header section.+                                    case (rgheadersequencingcentertagp =~ [re|[C][N]|]) of+                                      False -> fail $ show SAM_V1_6_Error_Read_Group_Sequencing_Center_Incorrect_Format +                                      True  -> -- CN tag is in the accepted format. +                                               return rgheadersequencingcentertagp+  _ <- word8 58+  rgheadersequencingcentervalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Read_Group_Sequencing_Center { sam_v1_6_read_group_sequencing_center_tag   = DSeq.fromList $ DB.unpack rgheadersequencingcentertag+                                               , sam_v1_6_read_group_sequencing_center_value = rgheadersequencingcentervalue+                                               }
+ src/Data/SAM/Version1_6/Read/Parser/Header/RG/DS.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.RG.DS+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.RG.DS ( -- * SAM_V1_6 parser - header section (Read group) - DS tag+                                                      parse_SAM_V1_6_SAM_V1_6_Read_Group_DS+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the DS tag of the @RG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Read_Group_DS :: Parser SAM_V1_6_Read_Group_Description +parse_SAM_V1_6_SAM_V1_6_Read_Group_DS = do+  rgheaderdescriptiontag <- do rgheaderdescriptiontagp <- DABL.takeTill (== 58)+                               -- Parse DS tag of the header section.+                               case (rgheaderdescriptiontagp =~ [re|[D][S]|]) of+                                 False -> fail $ show SAM_V1_6_Error_Read_Group_Description_Incorrect_Format +                                 True  -> -- DS tag is in the accepted format. +                                          return rgheaderdescriptiontagp+  _ <- word8 58+  rgheaderdescriptionvalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Read_Group_Description { sam_v1_6_read_group_description_tag   = DSeq.fromList $ DB.unpack rgheaderdescriptiontag+                                         , sam_v1_6_read_group_description_value = rgheaderdescriptionvalue+                                         }
+ src/Data/SAM/Version1_6/Read/Parser/Header/RG/DT.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.RG.DT+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.RG.DT ( -- * SAM_V1_6 parser - header section (Read group) - DT tag+                                                      parse_SAM_V1_6_SAM_V1_6_Read_Group_DT+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DTeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the DT tag of the @RG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Read_Group_DT :: Parser SAM_V1_6_Read_Group_Run_Date +parse_SAM_V1_6_SAM_V1_6_Read_Group_DT = do+  rgheaderrundatetag <- do rgheaderrundatetagp <- DABL.takeTill (== 58)+                           -- Parse DT tag of the header section.+                           case (rgheaderrundatetagp =~ [re|[D][T]|]) of+                             False -> fail $ show SAM_V1_6_Error_Read_Group_Date_Run_Produced_Incorrect_Format+                             True  -> -- DT tag is in the accepted format. +                                      return rgheaderrundatetagp+  _ <- word8 58+  rgheaderrundatevalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Read_Group_Run_Date { sam_v1_6_read_group_run_date_tag   = DTeq.fromList $ DB.unpack rgheaderrundatetag+                                      , sam_v1_6_read_group_run_date_value = rgheaderrundatevalue+                                      }
+ src/Data/SAM/Version1_6/Read/Parser/Header/RG/FO.hs view
@@ -0,0 +1,75 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.RG.FO+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.RG.FO ( -- * SAM_V1_6 parser - header section (Read group) - FO tag+                                                      parse_SAM_V1_6_SAM_V1_6_Read_Group_FO+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the FO tag of the @RG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Read_Group_FO :: Parser SAM_V1_6_Read_Group_Flow_Order +parse_SAM_V1_6_SAM_V1_6_Read_Group_FO = do+  rgheaderflowordertag <- do rgheaderflowordertagp <- DABL.takeTill (== 58)+                             -- Parse FO tag of the header section.+                             case (rgheaderflowordertagp =~ [re|[F][O]|]) of+                               False -> fail $ show SAM_V1_6_Error_Read_Group_Flow_Order_Incorrect_Format+                               True  -> -- FO tag is in the accepted format. +                                        return rgheaderflowordertagp+  _ <- word8 58+  rgheaderflowordervalue <- do rgheaderflowordervaluep <- DABL.takeTill (== 09)+                               -- Parse FO value of the header section.+                               case (rgheaderflowordervaluep =~ [re|/\*|[ACMGRSVTWYHKDBN]+/|]) of+                                 False -> fail $ show SAM_V1_6_Error_Read_Group_Flow_Order_Incorrect_Format+                                 True  -> -- FO value is in the accepted format.+                                          return rgheaderflowordervaluep+  return SAM_V1_6_Read_Group_Flow_Order { sam_v1_6_read_group_flow_order_tag   = DSeq.fromList $ DB.unpack rgheaderflowordertag+                                        , sam_v1_6_read_group_flow_order_value = rgheaderflowordervalue+                                        }
+ src/Data/SAM/Version1_6/Read/Parser/Header/RG/ID.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.RG.ID+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.RG.ID ( -- * SAM_V1_6 parser - header section (Read group) - ID tag+                                                      parse_SAM_V1_6_SAM_V1_6_Read_Group_ID+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the ID tag of the @RG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Read_Group_ID :: Parser SAM_V1_6_Read_Group_Identifier +parse_SAM_V1_6_SAM_V1_6_Read_Group_ID = do+  rgheaderreadgroupidentifiertag <- do rgheaderreadgroupidentifiertagp <- DABL.takeTill (== 58)+                                       -- Parse ID tag of the header section.+                                       case (rgheaderreadgroupidentifiertagp =~ [re|[I][D]|]) of+                                         False -> fail $ show SAM_V1_6_Error_Read_Group_Read_Group_Identifier_Incorrect_Format+                                         True  -> -- ID tag is in the accepted format. +                                                  return rgheaderreadgroupidentifiertagp+  _ <- word8 58+  rgheaderreadgroupidentifiervalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Read_Group_Identifier { sam_v1_6_read_group_identifier_tag   = DSeq.fromList $ DB.unpack rgheaderreadgroupidentifiertag+                                        , sam_v1_6_read_group_identifier_value = rgheaderreadgroupidentifiervalue+                                        }
+ src/Data/SAM/Version1_6/Read/Parser/Header/RG/KS.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.RG.KS+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.RG.KS ( -- * SAM_V1_6 parser - header section (Read group) - KS tag+                                                      parse_SAM_V1_6_SAM_V1_6_Read_Group_KS+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the KS tag of the @RG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Read_Group_KS :: Parser SAM_V1_6_Read_Group_Key_Sequence +parse_SAM_V1_6_SAM_V1_6_Read_Group_KS = do+  rgheaderkeysequencetag <- do rgheaderkeysequencetagp <- DABL.takeTill (== 58)+                               -- Parse KS tag of the header section.+                               case (rgheaderkeysequencetagp =~ [re|[K][S]|]) of+                                 False -> fail $ show SAM_V1_6_Error_Read_Group_Key_Sequence_Incorrect_Format+                                 True  -> -- KS tag is in the accepted format. +                                          return rgheaderkeysequencetagp+  _ <- word8 58+  rgheaderkeysequencevalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Read_Group_Key_Sequence { sam_v1_6_read_group_key_sequence_tag   = DSeq.fromList $ DB.unpack rgheaderkeysequencetag+                                          , sam_v1_6_read_group_key_sequence_value = rgheaderkeysequencevalue+                                          }
+ src/Data/SAM/Version1_6/Read/Parser/Header/RG/LB.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.RG.LB+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.RG.LB ( -- * SAM_V1_6 parser - header section (Read group) - LB tag+                                                      parse_SAM_V1_6_SAM_V1_6_Read_Group_LB+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the LB tag of the @RG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Read_Group_LB :: Parser SAM_V1_6_Read_Group_Library +parse_SAM_V1_6_SAM_V1_6_Read_Group_LB = do+  rgheaderlibrarytag <- do rgheaderlibrarytagp <- DABL.takeTill (== 58)+                           -- Parse LB tag of the header section.+                           case (rgheaderlibrarytagp =~ [re|[L][B]|]) of+                             False -> fail $ show SAM_V1_6_Error_Read_Group_Library_Incorrect_Format+                             True  -> -- LB tag is in the accepted format. +                                      return rgheaderlibrarytagp+  _ <- word8 58+  rgheaderlibraryvalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Read_Group_Library { sam_v1_6_read_group_library_tag   = DSeq.fromList $ DB.unpack rgheaderlibrarytag+                                     , sam_v1_6_read_group_library_value = rgheaderlibraryvalue+                                     }
+ src/Data/SAM/Version1_6/Read/Parser/Header/RG/PG.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.RG.PG+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.RG.PG ( -- * SAM_V1_6 parser - header section (Read group) - PG tag+                                                      parse_SAM_V1_6_SAM_V1_6_Read_Group_PG+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the PG tag of the @RG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Read_Group_PG :: Parser SAM_V1_6_Read_Group_Programs +parse_SAM_V1_6_SAM_V1_6_Read_Group_PG = do+  rgheaderprogramstag <- do rgheaderprogramstagp <- DABL.takeTill (== 58)+                            -- Parse PG tag of the header section.+                            case (rgheaderprogramstagp =~ [re|[P][G]|]) of+                              False -> fail $ show SAM_V1_6_Error_Read_Group_Programs_Incorrect_Format+                              True  -> -- PG tag is in the accepted format. +                                       return rgheaderprogramstagp+  _ <- word8 58+  rgheaderprogramsvalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Read_Group_Programs { sam_v1_6_read_group_programs_tag   = DSeq.fromList $ DB.unpack rgheaderprogramstag+                                      , sam_v1_6_read_group_programs_value = rgheaderprogramsvalue+                                      }
+ src/Data/SAM/Version1_6/Read/Parser/Header/RG/PI.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.RG.PI+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.RG.PI ( -- * SAM_V1_6 parser - header section (Read group) - PI tag+                                                      parse_SAM_V1_6_SAM_V1_6_Read_Group_PI+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the PI tag of the @RG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Read_Group_PI :: Parser SAM_V1_6_Read_Group_Predicted_Median_Insert_Size +parse_SAM_V1_6_SAM_V1_6_Read_Group_PI = do+  rgheaderpredictedmedianinsertsizetag <- do rgheaderpredictedmedianinsertsizetagp <- DABL.takeTill (== 58)+                                             -- Parse PI tag of the header section.+                                             case (rgheaderpredictedmedianinsertsizetagp =~ [re|[P][I]|]) of+                                               False -> fail $ show SAM_V1_6_Error_Read_Group_Predicted_Median_Insert_Size_Incorrect_Format+                                               True  -> -- PI tag is in the accepted format. +                                                        return rgheaderpredictedmedianinsertsizetagp+  _ <- word8 58+  rgheaderpredictedmedianinsertsizevalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Read_Group_Predicted_Median_Insert_Size { sam_v1_6_read_group_predicted_median_insert_size_tag   = DSeq.fromList $ DB.unpack rgheaderpredictedmedianinsertsizetag+                                                          , sam_v1_6_read_group_predicted_median_insert_size_value = rgheaderpredictedmedianinsertsizevalue+                                                          }
+ src/Data/SAM/Version1_6/Read/Parser/Header/RG/PL.hs view
@@ -0,0 +1,75 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.RG.PL+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.RG.PL ( -- * SAM_V1_6 parser - header section (Read group) - PL tag+                                                      parse_SAM_V1_6_SAM_V1_6_Read_Group_PL+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the PL tag of the @RG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Read_Group_PL :: Parser SAM_V1_6_Read_Group_Platform +parse_SAM_V1_6_SAM_V1_6_Read_Group_PL = do+  rgheaderplatformtag <- do rgheaderplatformtagp <- DABL.takeTill (== 58)+                            -- Parse PL tag of the header section.+                            case (rgheaderplatformtagp =~ [re|[P][L]|]) of+                              False -> fail $ show SAM_V1_6_Error_Read_Group_Platform_Incorrect_Format+                              True  -> -- PL tag is in the accepted format. +                                       return rgheaderplatformtagp+  _ <- word8 58+  rgheaderplatformvalue <- do rgheaderplatformvaluep <- DABL.takeTill (== 09)+                              -- Parse PL value of the header section.+                              case (rgheaderplatformvaluep =~ [re|[C][A][P][I][L][L][A][R][Y]|[D][N][B][S][E][Q]|[E][L][E][M][E][N][T]|[H][E][L][I][C][O][S]|[I][L][L][U][M][I][N][A]|[I][O][N][T][O][R][R][E][N][T]|[L][S][4][5][4]|[O][N][T]|[P][A][C][B][I][O]|[S][O][L][I][D]|[U][L][T][I][M][A]|]) of+                                False -> fail $ show SAM_V1_6_Error_Read_Group_Platform_Incorrect_Format+                                True  -> -- PL value is in the accepted format.+                                         return rgheaderplatformvaluep+  return SAM_V1_6_Read_Group_Platform { sam_v1_6_read_group_platform_tag   = DSeq.fromList $ DB.unpack rgheaderplatformtag+                                      , sam_v1_6_read_group_platform_value = rgheaderplatformvalue+                                      }
+ src/Data/SAM/Version1_6/Read/Parser/Header/RG/PM.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.RG.PM+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.RG.PM ( -- * SAM_V1_6 parser - header section (Read group) - PM tag+                                                      parse_SAM_V1_6_SAM_V1_6_Read_Group_PM+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the PM tag of the @RG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Read_Group_PM :: Parser SAM_V1_6_Read_Group_Platform_Model +parse_SAM_V1_6_SAM_V1_6_Read_Group_PM = do+  rgheaderplatformmodeltag <- do rgheaderplatformmodeltagp <- DABL.takeTill (== 58)+                                 -- Parse PM tag of the header section.+                                 case (rgheaderplatformmodeltagp =~ [re|[P][M]|]) of+                                   False -> fail $ show SAM_V1_6_Error_Read_Group_Platform_Model_Incorrect_Format+                                   True  -> -- PM tag is in the accepted format. +                                            return rgheaderplatformmodeltagp+  _ <- word8 58+  rgheaderplatformmodelvalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Read_Group_Platform_Model { sam_v1_6_read_group_platform_model_tag   = DSeq.fromList $ DB.unpack rgheaderplatformmodeltag+                                            , sam_v1_6_read_group_platform_model_value = rgheaderplatformmodelvalue+                                            }
+ src/Data/SAM/Version1_6/Read/Parser/Header/RG/PU.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.RG.PU+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.RG.PU ( -- * SAM_V1_6 parser - header section (Read group) - PU tag+                                                      parse_SAM_V1_6_SAM_V1_6_Read_Group_PU+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the PU tag of the @RG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Read_Group_PU :: Parser SAM_V1_6_Read_Group_Platform_Unit +parse_SAM_V1_6_SAM_V1_6_Read_Group_PU = do+  rgheaderplatformunittag <- do rgheaderplatformunittagp <- DABL.takeTill (== 58)+                                -- Parse PU tag of the header section.+                                case (rgheaderplatformunittagp =~ [re|[P][U]|]) of+                                  False -> fail $ show SAM_V1_6_Error_Read_Group_Platform_Unit_Incorrect_Format +                                  True  -> -- PU tag is in the accepted format. +                                           return rgheaderplatformunittagp+  _ <- word8 58+  rgheaderplatformunitvalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Read_Group_Platform_Unit { sam_v1_6_read_group_platform_unit_tag   = DSeq.fromList $ DB.unpack rgheaderplatformunittag+                                           , sam_v1_6_read_group_platform_unit_value = rgheaderplatformunitvalue+                                           }
+ src/Data/SAM/Version1_6/Read/Parser/Header/RG/SM.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.RG.SM+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.RG.SM ( -- * SAM_V1_6 parser - header section (Read group) - SM tag+                                                      parse_SAM_V1_6_SAM_V1_6_Read_Group_SM+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the SM tag of the @RG tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Read_Group_SM :: Parser SAM_V1_6_Read_Group_Sample +parse_SAM_V1_6_SAM_V1_6_Read_Group_SM = do+  rgheadersampletag <- do rgheadersampletagp <- DABL.takeTill (== 58)+                          -- Parse SM tag of the header section.+                          case (rgheadersampletagp =~ [re|[S][M]|]) of+                            False -> fail $ show SAM_V1_6_Error_Read_Group_Sample_Incorrect_Format+                            True  -> -- SM tag is in the accepted format. +                                     return rgheadersampletagp+  _ <- word8 58+  rgheadersamplevalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Read_Group_Sample { sam_v1_6_read_group_sample_tag   = DSeq.fromList $ DB.unpack rgheadersampletag+                                    , sam_v1_6_read_group_sample_value = rgheadersamplevalue+                                    }
+ src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AH.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.SQ.AH+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.SQ.AH ( -- * SAM_V1_6 parser - header section (Reference sequence dictionary) - AH tag+                                                      parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_AH+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the AH tag of the @SQ tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_AH :: Parser SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_AH = do+  sqheaderalternativelocustag <- do sqheaderalternativelocustagp <- DABL.takeTill (== 58)+                                    -- Parse AH tag of the header section.+                                    case (sqheaderalternativelocustagp =~ [re|[A][H]|]) of+                                      False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Alternative_Locus_Incorrect_Format+                                      True  -> -- AH tag is in the accepted format.+                                               return sqheaderalternativelocustagp+  _ <- word8 58+  sqheaderalternativelocusvalue <- DABL.takeTill (== 09) +  return SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus { sam_v1_6_reference_sequence_dictionary_alternative_locus_tag   = DSeq.fromList $ DB.unpack sqheaderalternativelocustag+                                                                  , sam_v1_6_reference_sequence_dictionary_alternative_locus_value = sqheaderalternativelocusvalue+                                                                  }
+ src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AN.hs view
@@ -0,0 +1,75 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.SQ.AN+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.SQ.AN ( -- * SAM_V1_6 parser - header section (Reference sequence dictionary) - AN tag+                                                      parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_AN+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the AN tag of the @SQ tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_AN :: Parser SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_AN = do+  sqheaderalternativereferencesequencenamestag <- do sqheaderalternativereferencesequencenamestagp <- DABL.takeTill (== 58)+                                                     -- Parse AN tag of the header section.+                                                     case (sqheaderalternativereferencesequencenamestagp =~ [re|[A][N]|]) of+                                                       False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names_Incorrect_Format+                                                       True  -> -- AN tag is in the accepted format.+                                                                return sqheaderalternativereferencesequencenamestagp+  _ <- word8 58+  sqheaderalternativereferencesequencenamesvalue <- do sqheaderalternativereferencesequencenamesvaluep <- DABL.takeTill (== 09)+                                                       -- Parse AN value of the header section.+                                                       case (sqheaderalternativereferencesequencenamesvaluep =~ [re|[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*(,[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*)*|]) of+                                                         False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names_Invalid_Value+                                                         True  -> -- AN value is in the accepted format.+                                                                  return sqheaderalternativereferencesequencenamesvaluep+  return SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names { sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_tag   = DSeq.fromList $ DB.unpack sqheaderalternativereferencesequencenamestag+                                                                                     , sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_value = sqheaderalternativereferencesequencenamesvalue+                                                                                     }
+ src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AS.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.SQ.AS+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.SQ.AS ( -- * SAM_V1_6 parser - header section (Reference sequence dictionary) - AS tag+                                                      parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_AS+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the AS tag of the @SQ tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_AS :: Parser SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_AS = do+  sqheadergenomeassemblyidentifiertag <- do sqheadergenomeassemblyidentifiertagp <- DABL.takeTill (== 58)+                                            -- Parse AS tag of the header section.+                                            case (sqheadergenomeassemblyidentifiertagp =~ [re|[A][S]|]) of+                                              False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Genome_Assembly_Identifier_Incorrect_Format+                                              True  -> -- AS tag is in the accepted format.+                                                       return sqheadergenomeassemblyidentifiertagp+  _ <- word8 58+  sqheadergenomeassemblyidentifiervalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier { sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tag   = DSeq.fromList $ DB.unpack sqheadergenomeassemblyidentifiertag+                                                                           , sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value = sqheadergenomeassemblyidentifiervalue+                                                                           }
+ src/Data/SAM/Version1_6/Read/Parser/Header/SQ/Base.hs view
@@ -0,0 +1,114 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.SQ.Base+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.SQ.Base ( -- * SAM_V1_6 parser - header section (Reference sequence dictionary)+                                                        parse_SAM_V1_6_Reference_Sequence_Dictionary+                                                      ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error+import Data.SAM.Version1_6.Read.Parser.Header.SQ.SN+import Data.SAM.Version1_6.Read.Parser.Header.SQ.LN+import Data.SAM.Version1_6.Read.Parser.Header.SQ.AH+import Data.SAM.Version1_6.Read.Parser.Header.SQ.AN+import Data.SAM.Version1_6.Read.Parser.Header.SQ.AS+import Data.SAM.Version1_6.Read.Parser.Header.SQ.DS+import Data.SAM.Version1_6.Read.Parser.Header.SQ.M5+import Data.SAM.Version1_6.Read.Parser.Header.SQ.SP+import Data.SAM.Version1_6.Read.Parser.Header.SQ.TP+import Data.SAM.Version1_6.Read.Parser.Header.SQ.UR++import Data.Attoparsec.ByteString.Lazy   as DABL+import Text.Regex.PCRE.Heavy++-- | Make a parser optional, return Nothing if there is no match.+maybeOption :: Parser a+            -> Parser (Maybe a)+maybeOption p = option Nothing (Just <$> p)++-- | @"SAM_V1_6_Reference_Sequence_Dictionary"@ parser.+--+-- Defines a parser for @SQ tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_Reference_Sequence_Dictionary :: Parser SAM_V1_6_Reference_Sequence_Dictionary+parse_SAM_V1_6_Reference_Sequence_Dictionary = do+  _         <- do sqheaderp <- DABL.takeTill (== 09)+                  -- Parse @SQ tag of the header section.+                  case (sqheaderp =~ [re|[@][S][Q]|]) of+                    False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Tag_Incorrect_Format+                    True  -> -- @SQ tag is in the accepted format.+                             return sqheaderp+  _         <- word8 09+  -- This parser assumes that the SN tag always appears first, followed by+  -- the LN tag, followed by the AH, AN, AS, DS, M5,+  -- SP, TP and UR tags if they exist, in that order.+  sn <- parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_SN+  _  <- word8 09+  ln <- parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_LN+  _  <- word8 09+  ah <- maybeOption parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_AH+  _  <- word8 09+  an <- maybeOption parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_AN+  _  <- word8 09+  as <- maybeOption parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_AS+  _  <- word8 09+  ds <- maybeOption parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_DS+  _  <- word8 09+  m5 <- maybeOption parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_M5+  _  <- word8 09+  sp <- maybeOption parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_SP+  _  <- word8 09+  tp <- maybeOption parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_TP+  _  <- word8 09+  ur <- maybeOption parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_UR +  return SAM_V1_6_Reference_Sequence_Dictionary { sam_v1_6_reference_sequence_dictionary_reference_sequence_name                        = sn  +                                                , sam_v1_6_reference_sequence_dictionary_reference_sequence_length                      = ln+                                                , sam_v1_6_reference_sequence_dictionary_reference_alternative_locus                    = ah+                                                , sam_v1_6_reference_sequence_dictionary_reference_alternative_reference_sequence_names = an+                                                , sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier                     = as+                                                , sam_v1_6_reference_sequence_dictionary_description                                    = ds+                                                , sam_v1_6_reference_sequence_dictionary_md5_checksum                                   = m5+                                                , sam_v1_6_reference_sequence_dictionary_species                                        = sp+                                                , sam_v1_6_reference_sequence_dictionary_molecule_topology                              = tp+                                                , sam_v1_6_reference_sequence_dictionary_uri                                            = ur+                                                }
+ src/Data/SAM/Version1_6/Read/Parser/Header/SQ/DS.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.SQ.DS+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.SQ.DS ( -- * SAM_V1_6 parser - header section (Reference sequence dictionary) - DS tag+                                                      parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_DS+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the DS tag of the @SQ tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_DS :: Parser SAM_V1_6_Reference_Sequence_Dictionary_Description+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_DS = do+  sqheaderdescriptiontag <- do sqheaderdescriptiontagp <- DABL.takeTill (== 58)+                               -- Parse DS tag of the header section.+                               case (sqheaderdescriptiontagp =~ [re|[D][S]|]) of+                                 False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Description_Incorrect_Format +                                 True  -> -- DS tag is in the accepted format.+                                          return sqheaderdescriptiontagp+  _ <- word8 58+  sqheaderdescriptionvalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Reference_Sequence_Dictionary_Description { sam_v1_6_reference_sequence_dictionary_description_tag   = DSeq.fromList $ DB.unpack sqheaderdescriptiontag+                                                            , sam_v1_6_reference_sequence_dictionary_description_value = sqheaderdescriptionvalue+                                                            }
+ src/Data/SAM/Version1_6/Read/Parser/Header/SQ/LN.hs view
@@ -0,0 +1,75 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.SQ.LN+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.SQ.LN ( -- * SAM_V1_6 parser - header section (Reference sequence dictionary) - LN tag+                                                      parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_LN+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the LN tag of the @SQ tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_LN :: Parser SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_LN = do+  sqheadersequencelengthtag <- do sqheadersequencelengthtagp <- DABL.takeTill (== 58)+                                  -- Parse LN tag of the header section.+                                  case (sqheadersequencelengthtagp =~ [re|[L][N]|]) of+                                    False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Length_Incorrect_Format+                                    True  -> -- LN tag is in the accepted format.+                                             return sqheadersequencelengthtagp+  _ <- word8 58+  sqheadersequencelengthvalue <- do sqheadersequencelengthvaluep <- DABL.takeTill (== 09)+                                    -- Parse LN value of the header section.+                                    case (sqheadersequencelengthvaluep =~ [re|[0-9]*|]) of -- Make this regex actually check the range of [1,2^31 - 1]?+                                      False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Length_Invalid_Value+                                      True  -> -- LN value is in the accepted format.+                                               return sqheadersequencelengthvaluep+  return SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length { sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tag   = DSeq.fromList $ DB.unpack sqheadersequencelengthtag+                                                                          , sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value = sqheadersequencelengthvalue+                                                                          }
+ src/Data/SAM/Version1_6/Read/Parser/Header/SQ/M5.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.SQ.M5+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.SQ.M5 ( -- * SAM_V1_6 parser - header section (Reference sequence dictionary) - M5 tag+                                                      parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_M5+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the M5 tag of the @SQ tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_M5 :: Parser SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_M5 = do+  sqheadermd5checksumtag <- do sqheadermd5checksumtagp <- DABL.takeTill (== 58)+                               -- Parse M5 tag of the header section.+                               case (sqheadermd5checksumtagp =~ [re|[M][5]|]) of+                                 False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_MD5_Checksum_Incorrect_Format +                                 True  -> -- M5 tag is in the accepted format.+                                          return sqheadermd5checksumtagp+  _ <- word8 58+  sqheadermd5checksumvalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum { sam_v1_6_reference_sequence_dictionary_md5_checksum_tag   = DSeq.fromList $ DB.unpack sqheadermd5checksumtag+                                                             , sam_v1_6_reference_sequence_dictionary_md5_checksum_value = sqheadermd5checksumvalue+                                                             }
+ src/Data/SAM/Version1_6/Read/Parser/Header/SQ/SN.hs view
@@ -0,0 +1,75 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.SQ.SN+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.SQ.SN ( -- * SAM_V1_6 parser - header section (Reference sequence dictionary) - SN tag+                                                      parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_SN+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the SN tag of the @SQ tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_SN :: Parser SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_SN = do+  sqheadersequencenametag <- do sqheadersequencenametagp <- DABL.takeTill (== 58)+                                -- Parse SN tag of the header section.+                                case (sqheadersequencenametagp =~ [re|[S][N]|]) of+                                  False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Name_Incorrect_Format+                                  True  -> -- SN tag is in the accepted format. +                                           return sqheadersequencenametagp+  _ <- word8 58+  sqheadersequencenamevalue <- do sqheadersequencenamevaluep <- DABL.takeTill (== 09)+                                  -- Parse SN value of the header section.+                                  case (sqheadersequencenamevaluep =~ [re|[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*|]) of+                                    False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Reference_Sequence_Name_Invalid_Value+                                    True  -> -- SN value is in the accepted format.+                                             return sqheadersequencenamevaluep  +  return SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name { sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tag   = DSeq.fromList $ DB.unpack sqheadersequencenametag+                                                                        , sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value = sqheadersequencenamevalue+                                                                        }
+ src/Data/SAM/Version1_6/Read/Parser/Header/SQ/SP.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.SQ.SP+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.SQ.SP ( -- * SAM_V1_6 parser - header section (Reference sequence dictionary) - SP tag+                                                      parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_SP+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the SP tag of the @SQ tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_SP :: Parser SAM_V1_6_Reference_Sequence_Dictionary_Species+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_SP = do+  sqheaderspeciestag <- do sqheaderspeciestagp <- DABL.takeTill (== 58)+                           -- Parse SP tag of the header section.+                           case (sqheaderspeciestagp =~ [re|[S][P]|]) of+                             False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Species_Incorrect_Format+                             True  -> -- SP tag is in the accepted format.+                                      return sqheaderspeciestagp+  _ <- word8 58+  sqheaderspeciesvalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Reference_Sequence_Dictionary_Species { sam_v1_6_reference_sequence_dictionary_species_tag   = DSeq.fromList $ DB.unpack sqheaderspeciestag+                                                        , sam_v1_6_reference_sequence_dictionary_species_value = sqheaderspeciesvalue+                                                        }
+ src/Data/SAM/Version1_6/Read/Parser/Header/SQ/TP.hs view
@@ -0,0 +1,75 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.SQ.TP+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.SQ.TP ( -- * SAM_V1_6 parser - header section (Reference sequence dictionary) - TP tag+                                                      parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_TP+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the TP tag of the @SQ tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_TP :: Parser SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_TP = do+  sqheadermoleculetopologytag <- do sqheadermoleculetopologytagp <- DABL.takeTill (== 58)+                                    -- Parse TP tag of the header section.+                                    case (sqheadermoleculetopologytagp =~ [re|[T][P]|]) of+                                      False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Molecule_Topology_Incorrect_Format+                                      True  -> -- TP tag is in the accepted format. +                                               return sqheadermoleculetopologytagp+  _ <- word8 58+  sqheadermoleculetopologyvalue <- do sqheadermoleculetopologyvaluep <- DABL.takeTill (== 09)+                                      -- Parse TP value of the header section.+                                      case (sqheadermoleculetopologyvaluep =~ [re|[l][i][n][e][a][r]|[c][i][r][c][u][l][a][r]|]) of+                                        False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_Molecule_Topology_Invalid_Value+                                        True  -> -- TP value is in the accepted format.+                                                 return sqheadermoleculetopologyvaluep  +  return SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology { sam_v1_6_reference_sequence_dictionary_molecule_topology_tag   = DSeq.fromList $ DB.unpack sqheadermoleculetopologytag+                                                                  , sam_v1_6_reference_sequence_dictionary_molecule_topology_value = sqheadermoleculetopologyvalue+                                                                  }
+ src/Data/SAM/Version1_6/Read/Parser/Header/SQ/UR.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE DeriveDataTypeable    #-}+{-# LANGUAGE DeriveGeneric         #-}+{-# LANGUAGE FlexibleContexts      #-}+{-# LANGUAGE FlexibleInstances     #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE OverloadedLists       #-}+{-# LANGUAGE OverloadedStrings     #-}+{-# LANGUAGE MultiWayIf            #-}+{-# LANGUAGE PackageImports        #-}+{-# LANGUAGE RecordWildCards       #-}+{-# LANGUAGE ScopedTypeVariables   #-}+{-# LANGUAGE TemplateHaskell       #-}+{-# LANGUAGE TypeFamilies          #-}+{-# LANGUAGE QuasiQuotes           #-}++-- |+-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.SQ.UR+-- Copyright   :  (c) Matthew Mosior 2023+-- 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.SAM.Version1_6.Read.Parser.Header.SQ.UR ( -- * SAM_V1_6 parser - header section (Reference sequence dictionary) - UR tag+                                                      parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_UR+                                                    ) where++import Data.SAM.Version1_6.Header+import Data.SAM.Version1_6.Read.Error++import           Data.Attoparsec.ByteString.Lazy   as DABL+import qualified Data.ByteString                   as DB   (unpack)+import           Data.Sequence                     as DSeq+import           Text.Regex.PCRE.Heavy++-- | Defines a parser for the UR tag of the @SQ tag section of the SAM v1.6 file format.+--+-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_UR :: Parser SAM_V1_6_Reference_Sequence_Dictionary_URI+parse_SAM_V1_6_SAM_V1_6_Reference_Sequence_Dictionary_UR = do+  sqheaderuritag <- do sqheaderuritagp <- DABL.takeTill (== 58)+                       -- Parse UR tag of the header section.+                       case (sqheaderuritagp =~ [re|[U][R]|]) of+                         False -> fail $ show SAM_V1_6_Error_Reference_Sequence_Dictionary_URI_Incorrect_Format+                         True  -> -- UR tag is in the accepted format.+                                  return sqheaderuritagp+  _ <- word8 58+  sqheaderurivalue <- DABL.takeTill (== 09)+  return SAM_V1_6_Reference_Sequence_Dictionary_URI { sam_v1_6_reference_sequence_dictionary_uri_tag   = DSeq.fromList $ DB.unpack sqheaderuritag+                                                    , sam_v1_6_reference_sequence_dictionary_uri_value = sqheaderurivalue+                                                    }
+ test/Main.hs view
@@ -0,0 +1,4 @@+module Main (main) where++main :: IO ()+main = putStrLn "Test suite not yet implemented."