{-# 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.HOPT
-- 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.HOPT ( -- * SAM_V1_6 parser - alignment section - hopt field 
                                                        parse_SAM_V1_6_Alignment_HOPT
                                                      ) where

import Data.SAM.Version1_6.Read.Error

import           Data.Attoparsec.ByteString.Lazy   as DABL
import qualified Data.ByteString                   as DB
import           Data.Sequence                     as DSeq
import           Data.Word
import           Text.Regex.PCRE.Heavy

-- | Defines a parser for the optional hopt 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_HOPT :: Parser (Seq Word8)
parse_SAM_V1_6_Alignment_HOPT :: Parser (Seq Word8)
parse_SAM_V1_6_Alignment_HOPT = do
  ByteString
_ <- do ByteString
alignmenthoptfieldtagp <- (Word8 -> Bool) -> Parser ByteString ByteString
DABL.takeTill (Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
58)
          -- Parse HOPT tag of the alignment section.
          case (ByteString
alignmenthoptfieldtagp 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
$ SAM_V1_6_Error -> String
forall a. Show a => a -> String
show SAM_V1_6_Error
SAM_V1_6_Error_Alignment_HOPT_Tag_Incorrect_Format
            Bool
True  -> -- HOPT 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
alignmenthoptfieldtagp
  Word8
_ <- Word8 -> Parser Word8
word8 Word8
58
  ByteString
_ <- do ByteString
alignmenthoptfieldtypep <- (Word8 -> Bool) -> Parser ByteString ByteString
DABL.takeTill (Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
58)
          -- Parse HOPT type of the alignment section.
          case (ByteString
alignmenthoptfieldtypep ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[H]|]) 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_Alignment_HOPT_Type_Incorrect_Format
            Bool
True  -> -- HOPT 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
alignmenthoptfieldtypep
  Word8
_ <- Word8 -> Parser Word8
word8 Word8
58
  Seq Word8
alignmenthoptfieldvalue <- do ByteString
alignmenthoptfieldvaluep <- (Word8 -> Bool) -> Parser ByteString ByteString
DABL.takeTill (Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
09)
                                -- Parse HOPT value of the alignment section.
                                case (ByteString
alignmenthoptfieldvaluep ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|([0-9A-F][0-9A-F])*|]) of
                                  Bool
False -> String -> Parser (Seq Word8)
forall a. String -> Parser ByteString a
forall (m :: * -> *) a. MonadFail m => String -> m a
fail (String -> Parser (Seq Word8)) -> String -> Parser (Seq Word8)
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_Alignment_HOPT_Value_Incorrect_Format
                                  Bool
True  -> -- HOPT value is in the accepted format.
                                           Seq Word8 -> Parser (Seq Word8)
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return (Seq Word8 -> Parser (Seq Word8))
-> Seq Word8 -> Parser (Seq Word8)
forall a b. (a -> b) -> a -> b
$ [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]
DB.unpack ByteString
alignmenthoptfieldvaluep
  Seq Word8 -> Parser (Seq Word8)
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return Seq Word8
alignmenthoptfieldvalue