{-# 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 :: Parser SAM_V1_6_One_Line_Comment
parse_SAM_V1_6_One_Line_Comment = do
  ByteString
_         <- do ByteString
coheaderp <- (Word8 -> Bool) -> Parser ByteString ByteString
DABL.takeTill (Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
09)
                  -- Parse @PG tag of the header section.
                  case (ByteString
coheaderp ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[@][C][O]|]) 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
$ SAM_V1_6_Error -> String
forall a. Show a => a -> String
show SAM_V1_6_Error
SAM_V1_6_Error_One_Line_Comment_Tag_Incorrect_Format
                    Bool
True  -> -- @CO 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
coheaderp
  Word8
_         <- Word8 -> Parser Word8
word8 Word8
09
  ByteString
value     <- (Word8 -> Bool) -> Parser ByteString ByteString
DABL.takeTill (\Word8
x -> Word8
x Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
13 Bool -> Bool -> Bool
|| Word8
x Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
10)
  SAM_V1_6_One_Line_Comment -> Parser SAM_V1_6_One_Line_Comment
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return SAM_V1_6_One_Line_Comment { sam_v1_6_one_line_comment_value :: ByteString
sam_v1_6_one_line_comment_value = ByteString
value
                                   }