{-# 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.SAM.Version1_6.Read.Parser.Alignment.OptionalFields.IOPT
-- 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.SAM.Version1_6.Read.Parser.Alignment.OptionalFields.IOPT ( -- * SAM_V1_6 parser - alignment section - iopt field 
                                                                       parse_SAM_V1_6_Alignment_OptionalFields_IOPT
                                                                     ) where

import Data.SAM.Version1_6.Alignment.OptionalFields.IOPT
import Data.SAM.Version1_6.Read.Error

import           Data.Attoparsec.ByteString.Char8  as DABC8 (isEndOfLine)
import           Data.Attoparsec.ByteString.Lazy   as DABL
import qualified Data.ByteString.Char8             as DBC8
import           Text.Regex.PCRE.Heavy

-- | Defines a parser for the optional iopt 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_OptionalFields_IOPT :: Parser SAM_V1_6_Alignment_OptionalFields_IOPT
parse_SAM_V1_6_Alignment_OptionalFields_IOPT :: Parser SAM_V1_6_Alignment_OptionalFields_IOPT
parse_SAM_V1_6_Alignment_OptionalFields_IOPT = do
  ByteString
alignmentioptfieldtag <- do
    ByteString
alignmentioptfieldtagp <-
      (Word8 -> Bool) -> Parser ByteString ByteString
DABL.takeTill (Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
58)
    -- Parse IOPT tag of the alignment section.
    case (ByteString
alignmentioptfieldtagp 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_IOPT_Tag_Incorrect_Format
      Bool
True  ->
        -- IOPT 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
alignmentioptfieldtagp
  Word8
_ <-
    Word8 -> Parser Word8
word8 Word8
58
  ()
_ <- do
    ByteString
alignmentioptfieldtypep <-
      (Word8 -> Bool) -> Parser ByteString ByteString
DABL.takeTill (Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
58)
    -- Parse IOPT type of the alignment section.
    case (ByteString
alignmentioptfieldtypep ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[i]|]) 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
$ SAM_V1_6_Error -> String
forall a. Show a => a -> String
show SAM_V1_6_Error
SAM_V1_6_Error_Alignment_IOPT_Type_Incorrect_Format
      Bool
True  ->
        -- IOPT type is in the accepted format.
        () -> Parser ByteString ()
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return ()
  Word8
_ <-
    Word8 -> Parser Word8
word8 Word8
58
  Integer
alignmentioptfieldvalue <- do
    ByteString
alignmentioptfieldvaluep <-
      (Word8 -> Bool) -> Parser ByteString ByteString
DABL.takeTill (\Word8
x -> Word8
x Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
09 Bool -> Bool -> Bool
|| Word8 -> Bool
isEndOfLine Word8
x)
    -- Parse IOPT value of the alignment section.
    case (ByteString
alignmentioptfieldvaluep ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[-+]?[0-9]+|]) of
      Bool
False ->
        String -> Parser ByteString Integer
forall a. String -> Parser ByteString a
forall (m :: * -> *) a. MonadFail m => String -> m a
fail (String -> Parser ByteString Integer)
-> String -> Parser ByteString Integer
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_IOPT_Value_Incorrect_Format
      Bool
True  ->
        -- IOPT value is in the accepted format.
        case (ByteString -> Maybe (Integer, ByteString)
DBC8.readInteger ByteString
alignmentioptfieldvaluep) of
          Maybe (Integer, ByteString)
Nothing                                 -> Integer -> Parser ByteString Integer
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return (-Integer
1)
          Just (Integer
alignmentioptfieldvalueinteger,ByteString
_) -> Integer -> Parser ByteString Integer
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return Integer
alignmentioptfieldvalueinteger
  SAM_V1_6_Alignment_OptionalFields_IOPT
-> Parser SAM_V1_6_Alignment_OptionalFields_IOPT
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return SAM_V1_6_Alignment_OptionalFields_IOPT
           { sam_v1_6_alignment_optionalfields_iopt_tag :: ByteString
sam_v1_6_alignment_optionalfields_iopt_tag   = ByteString
alignmentioptfieldtag
           , sam_v1_6_alignment_optionalfields_iopt_value :: Integer
sam_v1_6_alignment_optionalfields_iopt_value = Integer
alignmentioptfieldvalue
           }