{-# LANGUAGE DeriveDataTypeable    #-}
{-# LANGUAGE DeriveGeneric         #-}
{-# LANGUAGE FlexibleContexts      #-}
{-# LANGUAGE FlexibleInstances     #-}
{-# LANGUAGE MultiParamTypeClasses #-}
{-# LANGUAGE OverloadedLists       #-}
{-# LANGUAGE OverloadedStrings     #-}
{-# LANGUAGE MultiWayIf            #-}
{-# LANGUAGE RecordWildCards       #-}
{-# LANGUAGE ScopedTypeVariables   #-}
{-# LANGUAGE TypeFamilies          #-}
{-# Language QuasiQuotes           #-}

-- |
-- Module      :  Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BOPT
-- Copyright   :  (c) Matthew Mosior 2024
-- License     :  BSD-style
-- Maintainer  :  mattm.github@gmail.com
-- Portability :  portable
--
-- = WARNING
--
-- This module is considered __internal__.
--
-- The Package Versioning Policy __does not apply__.
--
-- The contents of this module may change __in any way whatsoever__
-- and __without any warning__ between minor versions of this package.
--
-- Authors importing this library are expected to track development
-- closely.
--
-- All credit goes to the author(s)/maintainer(s) of the
-- [containers](https://hackage.haskell.org/package/containers) library
-- for the above warning text.
--
-- = Description
--
-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.

module Data.BAM.Version1_6.Read.Parser.BAM.Alignment.OptionalFields.BOPT ( -- * BAM_V1_6_BAM parser - alignment section - bopt field 
                                                                           parse_BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
                                                                         ) where

import Data.BAM.Version1_6.BAM.Alignment.OptionalFields.BOPT
import Data.BAM.Version1_6.Internal
import Data.BAM.Version1_6.Read.Error

import           Data.Attoparsec.ByteString.Lazy as DABL
import qualified Data.ByteString                 as DB (unpack)
import qualified Data.ByteString.Char8           as DBC8
import           Data.Sequence                   as DSeq
import           Text.Regex.PCRE.Heavy

-- | Defines a parser for the optional bopt field of alignment section of the BAM v1.6 file format.
--
-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.
parse_BAM_V1_6_BAM_Alignment_OptionalFields_BOPT :: Parser BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
parse_BAM_V1_6_BAM_Alignment_OptionalFields_BOPT :: Parser BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
parse_BAM_V1_6_BAM_Alignment_OptionalFields_BOPT = do
  ByteString
alignmentboptfieldtag <- do
    ByteString
alignmentboptfieldtagp <-
      Int -> Parser ByteString ByteString
DABL.take Int
2
    -- Parse BOPT tag of the alignment section.
    case (ByteString
alignmentboptfieldtagp ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[A-Za-z][A-Za-z0-9]|]) of
      Bool
False ->
        String -> Parser ByteString ByteString
forall a. String -> Parser ByteString a
forall (m :: * -> *) a. MonadFail m => String -> m a
fail (String -> Parser ByteString ByteString)
-> String -> Parser ByteString ByteString
forall a b. (a -> b) -> a -> b
$
          BAM_V1_6_Read_Error -> String
forall a. Show a => a -> String
show BAM_V1_6_Read_Error
BAM_V1_6_Read_Error_Alignment_BOPT_Tag_Incorrect_Format
      Bool
True  ->
        -- BOPT tag is in the accepted format. 
        ByteString -> Parser ByteString ByteString
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return ByteString
alignmentboptfieldtagp
  ()
_ <- do
    ByteString
alignmentboptfieldtypep <-
      Int -> Parser ByteString ByteString
DABL.take Int
1
    -- Parse BOPT type of the alignment section.
    case (ByteString
alignmentboptfieldtypep ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[B]|]) of
      Bool
False ->
        String -> Parser ByteString ()
forall a. String -> Parser ByteString a
forall (m :: * -> *) a. MonadFail m => String -> m a
fail (String -> Parser ByteString ()) -> String -> Parser ByteString ()
forall a b. (a -> b) -> a -> b
$
          BAM_V1_6_Read_Error -> String
forall a. Show a => a -> String
show BAM_V1_6_Read_Error
BAM_V1_6_Read_Error_Alignment_BOPT_Type_Incorrect_Format
      Bool
True  ->
        -- BOPT type is in the accepted format.
        () -> Parser ByteString ()
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return ()
  ByteString
alignmentboptfieldvaluetype <- do
    ByteString
alignmentboptfieldvaluetypep <-
      Int -> Parser ByteString ByteString
DABL.take Int
1
    -- Parse BOPT value type of the alignment section.
    case (ByteString
alignmentboptfieldvaluetypep ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[cCsSiIf]|]) of
      Bool
False ->
        String -> Parser ByteString ByteString
forall a. String -> Parser ByteString a
forall (m :: * -> *) a. MonadFail m => String -> m a
fail (String -> Parser ByteString ByteString)
-> String -> Parser ByteString ByteString
forall a b. (a -> b) -> a -> b
$
          BAM_V1_6_Read_Error -> String
forall a. Show a => a -> String
show BAM_V1_6_Read_Error
BAM_V1_6_Read_Error_Alignment_BOPT_Value_Type_Incorrect_Format
      Bool
True  ->
        -- BOPT value type is in the accepted format.
        ByteString -> Parser ByteString ByteString
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return ByteString
alignmentboptfieldvaluetypep
  ByteString
alignmentboptfieldcount <-
    Int -> Parser ByteString ByteString
DABL.take Int
4
  case (ByteString -> String
DBC8.unpack ByteString
alignmentboptfieldvaluetype) of
    String
"c" -> do
      ByteString
alignmentboptfieldvaluedata <- do
        ByteString
alignmentboptfieldvaluedatap <-
          Int -> Parser ByteString ByteString
DABL.take (Int -> Parser ByteString ByteString)
-> Int -> Parser ByteString ByteString
forall a b. (a -> b) -> a -> b
$
            ( Word32 -> Int
forall a b. (Integral a, Num b) => a -> b
fromIntegral       (Word32 -> Int) -> Word32 -> Int
forall a b. (a -> b) -> a -> b
$
                [Word8] -> Word32
word8sToWord32LE ([Word8] -> Word32) -> [Word8] -> Word32
forall a b. (a -> b) -> a -> b
$
                  ByteString -> [Word8]
DB.unpack ByteString
alignmentboptfieldcount
            ) Int -> Int -> Int
forall a. Num a => a -> a -> a
* Int
1
        -- Parse BOPT value data of the alignment section.
        case (ByteString
alignmentboptfieldvaluedatap ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)*|]) of
          Bool
False ->
            String -> Parser ByteString ByteString
forall a. String -> Parser ByteString a
forall (m :: * -> *) a. MonadFail m => String -> m a
fail (String -> Parser ByteString ByteString)
-> String -> Parser ByteString ByteString
forall a b. (a -> b) -> a -> b
$
              BAM_V1_6_Read_Error -> String
forall a. Show a => a -> String
show BAM_V1_6_Read_Error
BAM_V1_6_Read_Error_Alignment_BOPT_Value_Data_Incorrect_Format
          Bool
True  ->
            -- BOPT value data is in the accepted format.
            ByteString -> Parser ByteString ByteString
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return ByteString
alignmentboptfieldvaluedatap 
      BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
-> Parser BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
               { bam_v1_6_bam_alignment_optionalfields_bopt_int8 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8
bam_v1_6_bam_alignment_optionalfields_bopt_int8   = BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8
-> Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8
forall a. a -> Maybe a
Just BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8
                                                                            { bam_v1_6_bam_alignment_optionalfields_bopt_int8_tag :: ByteString
bam_v1_6_bam_alignment_optionalfields_bopt_int8_tag   = ByteString
alignmentboptfieldtag
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_int8_type :: ByteString
bam_v1_6_bam_alignment_optionalfields_bopt_int8_type  = ByteString
alignmentboptfieldvaluetype
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_int8_count :: Word32
bam_v1_6_bam_alignment_optionalfields_bopt_int8_count = [Word8] -> Word32
word8sToWord32LE ([Word8] -> Word32) -> [Word8] -> Word32
forall a b. (a -> b) -> a -> b
$
                                                                                                                                        ByteString -> [Word8]
DB.unpack ByteString
alignmentboptfieldcount
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_int8_value :: Seq Int8
bam_v1_6_bam_alignment_optionalfields_bopt_int8_value = [Int8] -> Seq Int8
forall a. [a] -> Seq a
DSeq.fromList                      ([Int8] -> Seq Int8) -> [Int8] -> Seq Int8
forall a b. (a -> b) -> a -> b
$
                                                                                                                                        (ByteString -> Int8) -> [ByteString] -> [Int8]
forall a b. (a -> b) -> [a] -> [b]
map ([Word8] -> Int8
word8sToInt8LE ([Word8] -> Int8) -> (ByteString -> [Word8]) -> ByteString -> Int8
forall b c a. (b -> c) -> (a -> b) -> a -> c
. ByteString -> [Word8]
DB.unpack) ([ByteString] -> [Int8]) -> [ByteString] -> [Int8]
forall a b. (a -> b) -> a -> b
$
                                                                                                                                          Int -> ByteString -> [ByteString]
splitByteString Int
1
                                                                                                                                                          ByteString
alignmentboptfieldvaluedata
                                                                            }
               , bam_v1_6_bam_alignment_optionalfields_bopt_word8 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8
bam_v1_6_bam_alignment_optionalfields_bopt_word8  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_int16 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16
bam_v1_6_bam_alignment_optionalfields_bopt_int16  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word16 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16
bam_v1_6_bam_alignment_optionalfields_bopt_word16 = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_int32 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32
bam_v1_6_bam_alignment_optionalfields_bopt_int32  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word32 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32
bam_v1_6_bam_alignment_optionalfields_bopt_word32 = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_float :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float
bam_v1_6_bam_alignment_optionalfields_bopt_float  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float
forall a. Maybe a
Nothing
               }
    String
"C" -> do
      ByteString
alignmentboptfieldvaluedata <- do
        ByteString
alignmentboptfieldvaluedatap <-
          Int -> Parser ByteString ByteString
DABL.take (Int -> Parser ByteString ByteString)
-> Int -> Parser ByteString ByteString
forall a b. (a -> b) -> a -> b
$
            ( Word32 -> Int
forall a b. (Integral a, Num b) => a -> b
fromIntegral       (Word32 -> Int) -> Word32 -> Int
forall a b. (a -> b) -> a -> b
$
                [Word8] -> Word32
word8sToWord32LE ([Word8] -> Word32) -> [Word8] -> Word32
forall a b. (a -> b) -> a -> b
$
                  ByteString -> [Word8]
DB.unpack ByteString
alignmentboptfieldcount
            ) Int -> Int -> Int
forall a. Num a => a -> a -> a
* Int
1
        -- Parse BOPT value data of the alignment section.
        case (ByteString
alignmentboptfieldvaluedatap ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)*|]) of
          Bool
False ->
            String -> Parser ByteString ByteString
forall a. String -> Parser ByteString a
forall (m :: * -> *) a. MonadFail m => String -> m a
fail (String -> Parser ByteString ByteString)
-> String -> Parser ByteString ByteString
forall a b. (a -> b) -> a -> b
$
              BAM_V1_6_Read_Error -> String
forall a. Show a => a -> String
show BAM_V1_6_Read_Error
BAM_V1_6_Read_Error_Alignment_BOPT_Value_Data_Incorrect_Format
          Bool
True  ->
            -- BOPT value data is in the accepted format.
            ByteString -> Parser ByteString ByteString
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return ByteString
alignmentboptfieldvaluedatap
      BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
-> Parser BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
               { bam_v1_6_bam_alignment_optionalfields_bopt_int8 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8
bam_v1_6_bam_alignment_optionalfields_bopt_int8   = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word8 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8
bam_v1_6_bam_alignment_optionalfields_bopt_word8  = BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8
-> Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8
forall a. a -> Maybe a
Just BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8
                                                                            { bam_v1_6_bam_alignment_optionalfields_bopt_word8_tag :: ByteString
bam_v1_6_bam_alignment_optionalfields_bopt_word8_tag   = ByteString
alignmentboptfieldtag
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_word8_type :: ByteString
bam_v1_6_bam_alignment_optionalfields_bopt_word8_type  = ByteString
alignmentboptfieldvaluetype
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_word8_count :: Word32
bam_v1_6_bam_alignment_optionalfields_bopt_word8_count = [Word8] -> Word32
word8sToWord32LE ([Word8] -> Word32) -> [Word8] -> Word32
forall a b. (a -> b) -> a -> b
$
                                                                                                                                         ByteString -> [Word8]
DB.unpack ByteString
alignmentboptfieldcount
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_word8_value :: Seq Word8
bam_v1_6_bam_alignment_optionalfields_bopt_word8_value = [Word8] -> Seq Word8
forall a. [a] -> Seq a
DSeq.fromList                       ([Word8] -> Seq Word8) -> [Word8] -> Seq Word8
forall a b. (a -> b) -> a -> b
$
                                                                                                                                         (ByteString -> Word8) -> [ByteString] -> [Word8]
forall a b. (a -> b) -> [a] -> [b]
map ([Word8] -> Word8
word8sToWord8LE ([Word8] -> Word8)
-> (ByteString -> [Word8]) -> ByteString -> Word8
forall b c a. (b -> c) -> (a -> b) -> a -> c
. ByteString -> [Word8]
DB.unpack) ([ByteString] -> [Word8]) -> [ByteString] -> [Word8]
forall a b. (a -> b) -> a -> b
$
                                                                                                                                           Int -> ByteString -> [ByteString]
splitByteString Int
1
                                                                                                                                                           ByteString
alignmentboptfieldvaluedata
                                                                            }
               , bam_v1_6_bam_alignment_optionalfields_bopt_int16 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16
bam_v1_6_bam_alignment_optionalfields_bopt_int16  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word16 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16
bam_v1_6_bam_alignment_optionalfields_bopt_word16 = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_int32 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32
bam_v1_6_bam_alignment_optionalfields_bopt_int32  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word32 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32
bam_v1_6_bam_alignment_optionalfields_bopt_word32 = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_float :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float
bam_v1_6_bam_alignment_optionalfields_bopt_float  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float
forall a. Maybe a
Nothing
               }
    String
"s" -> do
      ByteString
alignmentboptfieldvaluedata <- do
        ByteString
alignmentboptfieldvaluedatap <-
          Int -> Parser ByteString ByteString
DABL.take (Int -> Parser ByteString ByteString)
-> Int -> Parser ByteString ByteString
forall a b. (a -> b) -> a -> b
$
            ( Word32 -> Int
forall a b. (Integral a, Num b) => a -> b
fromIntegral       (Word32 -> Int) -> Word32 -> Int
forall a b. (a -> b) -> a -> b
$
                [Word8] -> Word32
word8sToWord32LE ([Word8] -> Word32) -> [Word8] -> Word32
forall a b. (a -> b) -> a -> b
$
                  ByteString -> [Word8]
DB.unpack ByteString
alignmentboptfieldcount
            ) Int -> Int -> Int
forall a. Num a => a -> a -> a
* Int
2
        -- Parse BOPT value data of the alignment section.
        case (ByteString
alignmentboptfieldvaluedatap ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)*|]) of
          Bool
False ->
            String -> Parser ByteString ByteString
forall a. String -> Parser ByteString a
forall (m :: * -> *) a. MonadFail m => String -> m a
fail (String -> Parser ByteString ByteString)
-> String -> Parser ByteString ByteString
forall a b. (a -> b) -> a -> b
$
              BAM_V1_6_Read_Error -> String
forall a. Show a => a -> String
show BAM_V1_6_Read_Error
BAM_V1_6_Read_Error_Alignment_BOPT_Value_Data_Incorrect_Format
          Bool
True  ->
            -- BOPT value data is in the accepted format.
            ByteString -> Parser ByteString ByteString
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return ByteString
alignmentboptfieldvaluedatap
      BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
-> Parser BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
               { bam_v1_6_bam_alignment_optionalfields_bopt_int8 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8
bam_v1_6_bam_alignment_optionalfields_bopt_int8   = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word8 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8
bam_v1_6_bam_alignment_optionalfields_bopt_word8  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_int16 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16
bam_v1_6_bam_alignment_optionalfields_bopt_int16  = BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16
-> Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16
forall a. a -> Maybe a
Just BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16
                                                                            { bam_v1_6_bam_alignment_optionalfields_bopt_int16_tag :: ByteString
bam_v1_6_bam_alignment_optionalfields_bopt_int16_tag   = ByteString
alignmentboptfieldtag
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_int16_type :: ByteString
bam_v1_6_bam_alignment_optionalfields_bopt_int16_type  = ByteString
alignmentboptfieldvaluetype
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_int16_count :: Word32
bam_v1_6_bam_alignment_optionalfields_bopt_int16_count = [Word8] -> Word32
word8sToWord32LE ([Word8] -> Word32) -> [Word8] -> Word32
forall a b. (a -> b) -> a -> b
$
                                                                                                                                         ByteString -> [Word8]
DB.unpack ByteString
alignmentboptfieldcount
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_int16_value :: Seq Int16
bam_v1_6_bam_alignment_optionalfields_bopt_int16_value = [Int16] -> Seq Int16
forall a. [a] -> Seq a
DSeq.fromList                       ([Int16] -> Seq Int16) -> [Int16] -> Seq Int16
forall a b. (a -> b) -> a -> b
$
                                                                                                                                         (ByteString -> Int16) -> [ByteString] -> [Int16]
forall a b. (a -> b) -> [a] -> [b]
map ([Word8] -> Int16
word8sToInt16LE ([Word8] -> Int16)
-> (ByteString -> [Word8]) -> ByteString -> Int16
forall b c a. (b -> c) -> (a -> b) -> a -> c
. ByteString -> [Word8]
DB.unpack) ([ByteString] -> [Int16]) -> [ByteString] -> [Int16]
forall a b. (a -> b) -> a -> b
$ 
                                                                                                                                           Int -> ByteString -> [ByteString]
splitByteString Int
2
                                                                                                                                                           ByteString
alignmentboptfieldvaluedata
                                                                            }
               , bam_v1_6_bam_alignment_optionalfields_bopt_word16 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16
bam_v1_6_bam_alignment_optionalfields_bopt_word16 = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_int32 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32
bam_v1_6_bam_alignment_optionalfields_bopt_int32  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word32 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32
bam_v1_6_bam_alignment_optionalfields_bopt_word32 = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_float :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float
bam_v1_6_bam_alignment_optionalfields_bopt_float  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float
forall a. Maybe a
Nothing
               }
    String
"S" -> do
      ByteString
alignmentboptfieldvaluedata <- do
        ByteString
alignmentboptfieldvaluedatap <-
          Int -> Parser ByteString ByteString
DABL.take (Int -> Parser ByteString ByteString)
-> Int -> Parser ByteString ByteString
forall a b. (a -> b) -> a -> b
$
            ( Word32 -> Int
forall a b. (Integral a, Num b) => a -> b
fromIntegral       (Word32 -> Int) -> Word32 -> Int
forall a b. (a -> b) -> a -> b
$
                [Word8] -> Word32
word8sToWord32LE ([Word8] -> Word32) -> [Word8] -> Word32
forall a b. (a -> b) -> a -> b
$
                  ByteString -> [Word8]
DB.unpack ByteString
alignmentboptfieldcount
            ) Int -> Int -> Int
forall a. Num a => a -> a -> a
* Int
2
        -- Parse BOPT value data of the alignment section.
        case (ByteString
alignmentboptfieldvaluedatap ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)*|]) of
          Bool
False ->
            String -> Parser ByteString ByteString
forall a. String -> Parser ByteString a
forall (m :: * -> *) a. MonadFail m => String -> m a
fail (String -> Parser ByteString ByteString)
-> String -> Parser ByteString ByteString
forall a b. (a -> b) -> a -> b
$
              BAM_V1_6_Read_Error -> String
forall a. Show a => a -> String
show BAM_V1_6_Read_Error
BAM_V1_6_Read_Error_Alignment_BOPT_Value_Data_Incorrect_Format
          Bool
True  ->
            -- BOPT value data is in the accepted format.
            ByteString -> Parser ByteString ByteString
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return ByteString
alignmentboptfieldvaluedatap
      BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
-> Parser BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
               { bam_v1_6_bam_alignment_optionalfields_bopt_int8 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8
bam_v1_6_bam_alignment_optionalfields_bopt_int8   = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word8 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8
bam_v1_6_bam_alignment_optionalfields_bopt_word8  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_int16 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16
bam_v1_6_bam_alignment_optionalfields_bopt_int16  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word16 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16
bam_v1_6_bam_alignment_optionalfields_bopt_word16 = BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16
-> Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16
forall a. a -> Maybe a
Just BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16
                                                                            { bam_v1_6_bam_alignment_optionalfields_bopt_word16_tag :: ByteString
bam_v1_6_bam_alignment_optionalfields_bopt_word16_tag   = ByteString
alignmentboptfieldtag
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_word16_type :: ByteString
bam_v1_6_bam_alignment_optionalfields_bopt_word16_type  = ByteString
alignmentboptfieldvaluetype
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_word16_count :: Word32
bam_v1_6_bam_alignment_optionalfields_bopt_word16_count = [Word8] -> Word32
word8sToWord32LE ([Word8] -> Word32) -> [Word8] -> Word32
forall a b. (a -> b) -> a -> b
$
                                                                                                                                          ByteString -> [Word8]
DB.unpack ByteString
alignmentboptfieldcount
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_word16_value :: Seq Word16
bam_v1_6_bam_alignment_optionalfields_bopt_word16_value = [Word16] -> Seq Word16
forall a. [a] -> Seq a
DSeq.fromList                        ([Word16] -> Seq Word16) -> [Word16] -> Seq Word16
forall a b. (a -> b) -> a -> b
$
                                                                                                                                          (ByteString -> Word16) -> [ByteString] -> [Word16]
forall a b. (a -> b) -> [a] -> [b]
map ([Word8] -> Word16
word8sToWord16LE ([Word8] -> Word16)
-> (ByteString -> [Word8]) -> ByteString -> Word16
forall b c a. (b -> c) -> (a -> b) -> a -> c
. ByteString -> [Word8]
DB.unpack) ([ByteString] -> [Word16]) -> [ByteString] -> [Word16]
forall a b. (a -> b) -> a -> b
$
                                                                                                                                            Int -> ByteString -> [ByteString]
splitByteString Int
2
                                                                                                                                                            ByteString
alignmentboptfieldvaluedata
                                                                            }
               , bam_v1_6_bam_alignment_optionalfields_bopt_int32 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32
bam_v1_6_bam_alignment_optionalfields_bopt_int32  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word32 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32
bam_v1_6_bam_alignment_optionalfields_bopt_word32 = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_float :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float
bam_v1_6_bam_alignment_optionalfields_bopt_float  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float
forall a. Maybe a
Nothing
               }
    String
"i" -> do
      ByteString
alignmentboptfieldvaluedata <- do
        ByteString
alignmentboptfieldvaluedatap <-
          Int -> Parser ByteString ByteString
DABL.take (Int -> Parser ByteString ByteString)
-> Int -> Parser ByteString ByteString
forall a b. (a -> b) -> a -> b
$
            ( Word32 -> Int
forall a b. (Integral a, Num b) => a -> b
fromIntegral       (Word32 -> Int) -> Word32 -> Int
forall a b. (a -> b) -> a -> b
$
                [Word8] -> Word32
word8sToWord32LE ([Word8] -> Word32) -> [Word8] -> Word32
forall a b. (a -> b) -> a -> b
$
                  ByteString -> [Word8]
DB.unpack ByteString
alignmentboptfieldcount
            ) Int -> Int -> Int
forall a. Num a => a -> a -> a
* Int
4
        -- Parse BOPT value data of the alignment section.
        case (ByteString
alignmentboptfieldvaluedatap ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)*|]) of
          Bool
False ->
            String -> Parser ByteString ByteString
forall a. String -> Parser ByteString a
forall (m :: * -> *) a. MonadFail m => String -> m a
fail (String -> Parser ByteString ByteString)
-> String -> Parser ByteString ByteString
forall a b. (a -> b) -> a -> b
$
              BAM_V1_6_Read_Error -> String
forall a. Show a => a -> String
show BAM_V1_6_Read_Error
BAM_V1_6_Read_Error_Alignment_BOPT_Value_Data_Incorrect_Format
          Bool
True  ->
            -- BOPT value data is in the accepted format.
            ByteString -> Parser ByteString ByteString
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return ByteString
alignmentboptfieldvaluedatap
      BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
-> Parser BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
               { bam_v1_6_bam_alignment_optionalfields_bopt_int8 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8
bam_v1_6_bam_alignment_optionalfields_bopt_int8   = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word8 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8
bam_v1_6_bam_alignment_optionalfields_bopt_word8  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_int16 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16
bam_v1_6_bam_alignment_optionalfields_bopt_int16  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word16 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16
bam_v1_6_bam_alignment_optionalfields_bopt_word16 = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_int32 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32
bam_v1_6_bam_alignment_optionalfields_bopt_int32  = BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32
-> Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32
forall a. a -> Maybe a
Just BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32
                                                                            { bam_v1_6_bam_alignment_optionalfields_bopt_int32_tag :: ByteString
bam_v1_6_bam_alignment_optionalfields_bopt_int32_tag   = ByteString
alignmentboptfieldtag
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_int32_type :: ByteString
bam_v1_6_bam_alignment_optionalfields_bopt_int32_type  = ByteString
alignmentboptfieldvaluetype
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_int32_count :: Word32
bam_v1_6_bam_alignment_optionalfields_bopt_int32_count = [Word8] -> Word32
word8sToWord32LE ([Word8] -> Word32) -> [Word8] -> Word32
forall a b. (a -> b) -> a -> b
$
                                                                                                                                         ByteString -> [Word8]
DB.unpack ByteString
alignmentboptfieldcount
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_int32_value :: Seq Int32
bam_v1_6_bam_alignment_optionalfields_bopt_int32_value = [Int32] -> Seq Int32
forall a. [a] -> Seq a
DSeq.fromList                       ([Int32] -> Seq Int32) -> [Int32] -> Seq Int32
forall a b. (a -> b) -> a -> b
$
                                                                                                                                         (ByteString -> Int32) -> [ByteString] -> [Int32]
forall a b. (a -> b) -> [a] -> [b]
map ([Word8] -> Int32
word8sToInt32LE ([Word8] -> Int32)
-> (ByteString -> [Word8]) -> ByteString -> Int32
forall b c a. (b -> c) -> (a -> b) -> a -> c
. ByteString -> [Word8]
DB.unpack) ([ByteString] -> [Int32]) -> [ByteString] -> [Int32]
forall a b. (a -> b) -> a -> b
$
                                                                                                                                           Int -> ByteString -> [ByteString]
splitByteString Int
4
                                                                                                                                                           ByteString
alignmentboptfieldvaluedata
                                                                            }
               , bam_v1_6_bam_alignment_optionalfields_bopt_word32 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32
bam_v1_6_bam_alignment_optionalfields_bopt_word32 = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_float :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float
bam_v1_6_bam_alignment_optionalfields_bopt_float  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float
forall a. Maybe a
Nothing
               }
    String
"I" -> do
      ByteString
alignmentboptfieldvaluedata <- do
        ByteString
alignmentboptfieldvaluedatap <-
          Int -> Parser ByteString ByteString
DABL.take (Int -> Parser ByteString ByteString)
-> Int -> Parser ByteString ByteString
forall a b. (a -> b) -> a -> b
$
            ( Word32 -> Int
forall a b. (Integral a, Num b) => a -> b
fromIntegral       (Word32 -> Int) -> Word32 -> Int
forall a b. (a -> b) -> a -> b
$
                [Word8] -> Word32
word8sToWord32LE ([Word8] -> Word32) -> [Word8] -> Word32
forall a b. (a -> b) -> a -> b
$
                  ByteString -> [Word8]
DB.unpack ByteString
alignmentboptfieldcount
            ) Int -> Int -> Int
forall a. Num a => a -> a -> a
* Int
4
        -- Parse BOPT value data of the alignment section.
        case (ByteString
alignmentboptfieldvaluedatap ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)*|]) of
          Bool
False ->
            String -> Parser ByteString ByteString
forall a. String -> Parser ByteString a
forall (m :: * -> *) a. MonadFail m => String -> m a
fail (String -> Parser ByteString ByteString)
-> String -> Parser ByteString ByteString
forall a b. (a -> b) -> a -> b
$
              BAM_V1_6_Read_Error -> String
forall a. Show a => a -> String
show BAM_V1_6_Read_Error
BAM_V1_6_Read_Error_Alignment_BOPT_Value_Data_Incorrect_Format
          Bool
True  ->
            -- BOPT value data is in the accepted format.
            ByteString -> Parser ByteString ByteString
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return ByteString
alignmentboptfieldvaluedatap
      BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
-> Parser BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
               { bam_v1_6_bam_alignment_optionalfields_bopt_int8 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8
bam_v1_6_bam_alignment_optionalfields_bopt_int8   = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word8 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8
bam_v1_6_bam_alignment_optionalfields_bopt_word8  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_int16 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16
bam_v1_6_bam_alignment_optionalfields_bopt_int16  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word16 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16
bam_v1_6_bam_alignment_optionalfields_bopt_word16 = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_int32 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32
bam_v1_6_bam_alignment_optionalfields_bopt_int32  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word32 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32
bam_v1_6_bam_alignment_optionalfields_bopt_word32 = BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32
-> Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32
forall a. a -> Maybe a
Just BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32
                                                                            { bam_v1_6_bam_alignment_optionalfields_bopt_word32_tag :: ByteString
bam_v1_6_bam_alignment_optionalfields_bopt_word32_tag   = ByteString
alignmentboptfieldtag
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_word32_type :: ByteString
bam_v1_6_bam_alignment_optionalfields_bopt_word32_type  = ByteString
alignmentboptfieldvaluetype
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_word32_count :: Word32
bam_v1_6_bam_alignment_optionalfields_bopt_word32_count = [Word8] -> Word32
word8sToWord32LE ([Word8] -> Word32) -> [Word8] -> Word32
forall a b. (a -> b) -> a -> b
$
                                                                                                                                          ByteString -> [Word8]
DB.unpack ByteString
alignmentboptfieldcount
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_word32_value :: Seq Word32
bam_v1_6_bam_alignment_optionalfields_bopt_word32_value = [Word32] -> Seq Word32
forall a. [a] -> Seq a
DSeq.fromList                        ([Word32] -> Seq Word32) -> [Word32] -> Seq Word32
forall a b. (a -> b) -> a -> b
$
                                                                                                                                          (ByteString -> Word32) -> [ByteString] -> [Word32]
forall a b. (a -> b) -> [a] -> [b]
map ([Word8] -> Word32
word8sToWord32LE ([Word8] -> Word32)
-> (ByteString -> [Word8]) -> ByteString -> Word32
forall b c a. (b -> c) -> (a -> b) -> a -> c
. ByteString -> [Word8]
DB.unpack) ([ByteString] -> [Word32]) -> [ByteString] -> [Word32]
forall a b. (a -> b) -> a -> b
$
                                                                                                                                            Int -> ByteString -> [ByteString]
splitByteString Int
4
                                                                                                                                                            ByteString
alignmentboptfieldvaluedata
                                                                            }
               , bam_v1_6_bam_alignment_optionalfields_bopt_float :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float
bam_v1_6_bam_alignment_optionalfields_bopt_float  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float
forall a. Maybe a
Nothing
               }
    String
"f" -> do
      ByteString
alignmentboptfieldvaluedata <- do
        ByteString
alignmentboptfieldvaluedatap <-
          Int -> Parser ByteString ByteString
DABL.take (Int -> Parser ByteString ByteString)
-> Int -> Parser ByteString ByteString
forall a b. (a -> b) -> a -> b
$
            ( Word32 -> Int
forall a b. (Integral a, Num b) => a -> b
fromIntegral       (Word32 -> Int) -> Word32 -> Int
forall a b. (a -> b) -> a -> b
$
                [Word8] -> Word32
word8sToWord32LE ([Word8] -> Word32) -> [Word8] -> Word32
forall a b. (a -> b) -> a -> b
$
                  ByteString -> [Word8]
DB.unpack ByteString
alignmentboptfieldcount
            ) Int -> Int -> Int
forall a. Num a => a -> a -> a
* Int
4
        -- Parse BOPT value data of the alignment section.
        case (ByteString
alignmentboptfieldvaluedatap ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)*|]) of
          Bool
False ->
            String -> Parser ByteString ByteString
forall a. String -> Parser ByteString a
forall (m :: * -> *) a. MonadFail m => String -> m a
fail (String -> Parser ByteString ByteString)
-> String -> Parser ByteString ByteString
forall a b. (a -> b) -> a -> b
$
              BAM_V1_6_Read_Error -> String
forall a. Show a => a -> String
show BAM_V1_6_Read_Error
BAM_V1_6_Read_Error_Alignment_BOPT_Value_Data_Incorrect_Format
          Bool
True  ->
            -- BOPT value data is in the accepted format.
            ByteString -> Parser ByteString ByteString
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return ByteString
alignmentboptfieldvaluedatap
      BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
-> Parser BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
               { bam_v1_6_bam_alignment_optionalfields_bopt_int8 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8
bam_v1_6_bam_alignment_optionalfields_bopt_int8   = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word8 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8
bam_v1_6_bam_alignment_optionalfields_bopt_word8  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_int16 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16
bam_v1_6_bam_alignment_optionalfields_bopt_int16  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word16 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16
bam_v1_6_bam_alignment_optionalfields_bopt_word16 = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_int32 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32
bam_v1_6_bam_alignment_optionalfields_bopt_int32  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word32 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32
bam_v1_6_bam_alignment_optionalfields_bopt_word32 = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_float :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float
bam_v1_6_bam_alignment_optionalfields_bopt_float  = BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float
-> Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float
forall a. a -> Maybe a
Just BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float
                                                                            { bam_v1_6_bam_alignment_optionalfields_bopt_float_tag :: ByteString
bam_v1_6_bam_alignment_optionalfields_bopt_float_tag   = ByteString
alignmentboptfieldtag
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_float_type :: ByteString
bam_v1_6_bam_alignment_optionalfields_bopt_float_type  = ByteString
alignmentboptfieldvaluetype
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_float_count :: Word32
bam_v1_6_bam_alignment_optionalfields_bopt_float_count = [Word8] -> Word32
word8sToWord32LE ([Word8] -> Word32) -> [Word8] -> Word32
forall a b. (a -> b) -> a -> b
$
                                                                                                                                         ByteString -> [Word8]
DB.unpack ByteString
alignmentboptfieldcount
                                                                            , bam_v1_6_bam_alignment_optionalfields_bopt_float_value :: Seq Float
bam_v1_6_bam_alignment_optionalfields_bopt_float_value = [Float] -> Seq Float
forall a. [a] -> Seq a
DSeq.fromList             ([Float] -> Seq Float) -> [Float] -> Seq Float
forall a b. (a -> b) -> a -> b
$
                                                                                                                                         (ByteString -> Float) -> [ByteString] -> [Float]
forall a b. (a -> b) -> [a] -> [b]
map ByteString -> Float
bytestringToFloatLE ([ByteString] -> [Float]) -> [ByteString] -> [Float]
forall a b. (a -> b) -> a -> b
$
                                                                                                                                           Int -> ByteString -> [ByteString]
splitByteString Int
4
                                                                                                                                                           ByteString
alignmentboptfieldvaluedata
                                                                            }
               }
    String
_   ->
      BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
-> Parser BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
               { bam_v1_6_bam_alignment_optionalfields_bopt_int8 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8
bam_v1_6_bam_alignment_optionalfields_bopt_int8   = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int8
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word8 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8
bam_v1_6_bam_alignment_optionalfields_bopt_word8  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word8
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_int16 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16
bam_v1_6_bam_alignment_optionalfields_bopt_int16  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int16
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word16 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16
bam_v1_6_bam_alignment_optionalfields_bopt_word16 = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word16
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_int32 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32
bam_v1_6_bam_alignment_optionalfields_bopt_int32  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Int32
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_word32 :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32
bam_v1_6_bam_alignment_optionalfields_bopt_word32 = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Word32
forall a. Maybe a
Nothing
               , bam_v1_6_bam_alignment_optionalfields_bopt_float :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float
bam_v1_6_bam_alignment_optionalfields_bopt_float  = Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT_Float
forall a. Maybe a
Nothing
               }