{-# 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
}