hs-samtools-0.8.0.0: src/Data/SAM/Version1_6/Read/Base.hs
{-# LANGUAGE FlexibleContexts #-}
{-# LANGUAGE FlexibleInstances #-}
{-# LANGUAGE MultiParamTypeClasses #-}
{-# LANGUAGE TypeFamilies #-}
-- |
-- 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 Control.Applicative.Permutations (intercalateEffect,toPermutationWithDefault)
import Data.Attoparsec.ByteString.Char8 as DABC8 (endOfLine)
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
case filelevelmetadata of
Nothing -> do samwoalignment <- intercalateEffect endOfLine $
(,,,)
<$> toPermutationWithDefault Nothing
(Just <$> DABL.many1' parse_SAM_V1_6_Reference_Sequence_Dictionary)
<*> toPermutationWithDefault Nothing
(Just <$> DABL.many1' parse_SAM_V1_6_Read_Group)
<*> toPermutationWithDefault Nothing
(Just <$> parse_SAM_V1_6_Program)
<*> toPermutationWithDefault Nothing
(Just <$> DABL.many1' parse_SAM_V1_6_One_Line_Comment)
alignment <- DABL.many1' parse_SAM_V1_6_Alignment
return SAM_V1_6 { sam_v1_6_file_level_metadata = Nothing
, sam_v1_6_reference_sequence_dictionary = (\(a,_,_,_) -> case a of
Nothing -> Nothing
Just finala -> Just $ DSeq.fromList finala
) samwoalignment
, sam_v1_6_read_group = (\(_,b,_,_) -> case b of
Nothing -> Nothing
Just finalb -> Just $ DSeq.fromList finalb
) samwoalignment
, sam_v1_6_program = (\(_,_,c,_) -> c) samwoalignment
, sam_v1_6_one_line_comment = (\(_,_,_,d) -> case d of
Nothing -> Nothing
Just finald -> Just $ DSeq.fromList finald
) samwoalignment
, sam_v1_6_alignment = DSeq.fromList alignment
}
Just flm -> do samwoalignment <- intercalateEffect endOfLine $
(,,,)
<$> toPermutationWithDefault Nothing
(Just <$> DABL.many1' parse_SAM_V1_6_Reference_Sequence_Dictionary)
<*> toPermutationWithDefault Nothing
(Just <$> DABL.many1' parse_SAM_V1_6_Read_Group)
<*> toPermutationWithDefault Nothing
(Just <$> parse_SAM_V1_6_Program)
<*> toPermutationWithDefault Nothing
(Just <$> DABL.many1' parse_SAM_V1_6_One_Line_Comment)
alignment <- DABL.many1' parse_SAM_V1_6_Alignment
return SAM_V1_6 { sam_v1_6_file_level_metadata = Just flm
, sam_v1_6_reference_sequence_dictionary = (\(a,_,_,_) -> case a of
Nothing -> Nothing
Just finala -> Just $ DSeq.fromList finala
) samwoalignment
, sam_v1_6_read_group = (\(_,b,_,_) -> case b of
Nothing -> Nothing
Just finalb -> Just $ DSeq.fromList finalb
) samwoalignment
, sam_v1_6_program = (\(_,_,c,_) -> c) samwoalignment
, sam_v1_6_one_line_comment = (\(_,_,_,d) -> case d of
Nothing -> Nothing
Just finald -> Just $ DSeq.fromList finald
) samwoalignment
, 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 is parsed.
--
-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.
readSAM_V1_6 :: FilePath -- ^ Input 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