diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 --- /dev/null +++ b/CHANGELOG.md @@ -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. diff --git a/LICENSE b/LICENSE new file mode 100644 --- /dev/null +++ b/LICENSE @@ -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. diff --git a/hs-samtools.cabal b/hs-samtools.cabal new file mode 100644 --- /dev/null +++ b/hs-samtools.cabal @@ -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 diff --git a/src/Data/SAM/Version1_6/Alignment.hs b/src/Data/SAM/Version1_6/Alignment.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Alignment.hs @@ -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 diff --git a/src/Data/SAM/Version1_6/Alignment/BOPT.hs b/src/Data/SAM/Version1_6/Alignment/BOPT.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Alignment/BOPT.hs @@ -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) ++ + " }" diff --git a/src/Data/SAM/Version1_6/Alignment/Base.hs b/src/Data/SAM/Version1_6/Alignment/Base.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Alignment/Base.hs @@ -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]​(,[-+]?[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) ++ + " }" diff --git a/src/Data/SAM/Version1_6/Base.hs b/src/Data/SAM/Version1_6/Base.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Base.hs @@ -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) ++ + " }" diff --git a/src/Data/SAM/Version1_6/Header.hs b/src/Data/SAM/Version1_6/Header.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Header.hs @@ -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 diff --git a/src/Data/SAM/Version1_6/Header/CO.hs b/src/Data/SAM/Version1_6/Header/CO.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Header/CO.hs @@ -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) ++ + " }" diff --git a/src/Data/SAM/Version1_6/Header/HD.hs b/src/Data/SAM/Version1_6/Header/HD.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Header/HD.hs @@ -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) ++ + " }" diff --git a/src/Data/SAM/Version1_6/Header/PG.hs b/src/Data/SAM/Version1_6/Header/PG.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Header/PG.hs @@ -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) ++ + " }" diff --git a/src/Data/SAM/Version1_6/Header/RG.hs b/src/Data/SAM/Version1_6/Header/RG.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Header/RG.hs @@ -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) ++ + " }" diff --git a/src/Data/SAM/Version1_6/Header/SQ.hs b/src/Data/SAM/Version1_6/Header/SQ.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Header/SQ.hs @@ -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) ++ + " }" diff --git a/src/Data/SAM/Version1_6/Read/Base.hs b/src/Data/SAM/Version1_6/Read/Base.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Base.hs @@ -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 diff --git a/src/Data/SAM/Version1_6/Read/Error.hs b/src/Data/SAM/Version1_6/Read/Error.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Error.hs @@ -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) diff --git a/src/Data/SAM/Version1_6/Read/Parser/Alignment/AOPT.hs b/src/Data/SAM/Version1_6/Read/Parser/Alignment/AOPT.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Alignment/AOPT.hs @@ -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 diff --git a/src/Data/SAM/Version1_6/Read/Parser/Alignment/BOPT.hs b/src/Data/SAM/Version1_6/Read/Parser/Alignment/BOPT.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Alignment/BOPT.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Alignment/Base.hs b/src/Data/SAM/Version1_6/Read/Parser/Alignment/Base.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Alignment/Base.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Alignment/FOPT.hs b/src/Data/SAM/Version1_6/Read/Parser/Alignment/FOPT.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Alignment/FOPT.hs @@ -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 diff --git a/src/Data/SAM/Version1_6/Read/Parser/Alignment/HOPT.hs b/src/Data/SAM/Version1_6/Read/Parser/Alignment/HOPT.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Alignment/HOPT.hs @@ -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 diff --git a/src/Data/SAM/Version1_6/Read/Parser/Alignment/IOPT.hs b/src/Data/SAM/Version1_6/Read/Parser/Alignment/IOPT.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Alignment/IOPT.hs @@ -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 diff --git a/src/Data/SAM/Version1_6/Read/Parser/Alignment/ZOPT.hs b/src/Data/SAM/Version1_6/Read/Parser/Alignment/ZOPT.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Alignment/ZOPT.hs @@ -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 diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/CO/Base.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/CO/Base.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/CO/Base.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/HD/Base.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/HD/Base.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/HD/Base.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/HD/GO.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/HD/GO.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/HD/GO.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/HD/SO.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/HD/SO.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/HD/SO.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/HD/SS.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/HD/SS.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/HD/SS.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/HD/VN.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/HD/VN.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/HD/VN.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/Base.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/Base.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/Base.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/CL.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/CL.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/CL.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/DS.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/DS.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/DS.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/ID.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/ID.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/ID.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/PN.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/PN.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/PN.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/PP.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/PP.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/PP.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/PG/VN.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/VN.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/PG/VN.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/BC.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/BC.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/BC.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/Base.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/Base.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/Base.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/CN.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/CN.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/CN.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/DS.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/DS.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/DS.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/DT.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/DT.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/DT.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/FO.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/FO.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/FO.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/ID.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/ID.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/ID.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/KS.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/KS.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/KS.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/LB.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/LB.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/LB.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PG.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PG.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PG.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PI.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PI.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PI.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PL.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PL.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PL.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PM.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PM.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PM.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PU.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PU.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/PU.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/RG/SM.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/SM.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/RG/SM.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AH.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AH.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AH.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AN.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AN.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AN.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AS.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AS.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/AS.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/Base.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/Base.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/Base.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/DS.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/DS.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/DS.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/LN.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/LN.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/LN.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/M5.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/M5.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/M5.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/SN.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/SN.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/SN.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/SP.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/SP.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/SP.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/TP.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/TP.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/TP.hs @@ -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 + } diff --git a/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/UR.hs b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/UR.hs new file mode 100644 --- /dev/null +++ b/src/Data/SAM/Version1_6/Read/Parser/Header/SQ/UR.hs @@ -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 + } diff --git a/test/Main.hs b/test/Main.hs new file mode 100644 --- /dev/null +++ b/test/Main.hs @@ -0,0 +1,4 @@ +module Main (main) where + +main :: IO () +main = putStrLn "Test suite not yet implemented."