{-# 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.AOPT
-- 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.AOPT ( -- * BAM_V1_6_BAM parser - alignment section - aopt field 
                                                                           parse_BAM_V1_6_BAM_Alignment_OptionalFields_AOPT
                                                                         ) where

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

import           Data.ByteString                 as DB
import           Data.Attoparsec.ByteString.Lazy as DABL
import           Text.Regex.PCRE.Heavy

-- | Defines a parser for the optional aopt 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_AOPT :: Parser BAM_V1_6_BAM_Alignment_OptionalFields_AOPT
parse_BAM_V1_6_BAM_Alignment_OptionalFields_AOPT :: Parser BAM_V1_6_BAM_Alignment_OptionalFields_AOPT
parse_BAM_V1_6_BAM_Alignment_OptionalFields_AOPT = do
  ByteString
alignmentaoptfieldtag <- do
    ByteString
alignmentaoptfieldtagp <-
      Int -> Parser ByteString ByteString
DABL.take Int
2
    -- Parse AOPT tag of the alignment section.
    case (ByteString
alignmentaoptfieldtagp 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_AOPT_Tag_Incorrect_Format
      Bool
True  ->
        -- AOPT 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
alignmentaoptfieldtagp
  ()
_ <- do
    ByteString
alignmentaoptfieldtypep <-
      Int -> Parser ByteString ByteString
DABL.take Int
1
    -- Parse AOPT type of the alignment section.
    case (ByteString
alignmentaoptfieldtypep ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[A]|]) 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_AOPT_Type_Incorrect_Format
      Bool
True  ->
        -- AOPT type is in the accepted format.
        () -> Parser ByteString ()
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return ()
  ByteString
alignmentaoptfieldvalue <- do
    ByteString
alignmentaoptfieldvaluep <-
      Int -> Parser ByteString ByteString
DABL.take Int
1 
    -- Parse AOPT value of the alignment section.
    case (ByteString
alignmentaoptfieldvaluep ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[!-~]|]) 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_AOPT_Value_Incorrect_Format
      Bool
True  ->
        -- AOPT value 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
alignmentaoptfieldvaluep
  BAM_V1_6_BAM_Alignment_OptionalFields_AOPT
-> Parser BAM_V1_6_BAM_Alignment_OptionalFields_AOPT
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return BAM_V1_6_BAM_Alignment_OptionalFields_AOPT
           { bam_v1_6_bam_alignment_optionalfields_aopt_tag :: ByteString
bam_v1_6_bam_alignment_optionalfields_aopt_tag   = ByteString
alignmentaoptfieldtag
           , bam_v1_6_bam_alignment_optionalfields_aopt_value :: Word8
bam_v1_6_bam_alignment_optionalfields_aopt_value = [Word8] -> Word8
word8sToWord8LE ([Word8] -> Word8) -> [Word8] -> Word8
forall a b. (a -> b) -> a -> b
$
                                                                  ByteString -> [Word8]
DB.unpack ByteString
alignmentaoptfieldvalue
           }