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

-- |
-- Module      :  Data.SAM.Version1_6.Read.Parser.Header.RG.FO
-- 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.RG.FO ( -- * SAM_V1_6 parser - header section (Read group) - FO tag
                                                      parse_SAM_V1_6_Read_Group_FO
                                                    ) where

import Data.SAM.Version1_6.Header
import Data.SAM.Version1_6.Read.Error

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

-- | Defines a parser for the FO tag of the @RG 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_Read_Group_FO :: Parser SAM_V1_6_Read_Group_Flow_Order 
parse_SAM_V1_6_Read_Group_FO :: Parser SAM_V1_6_Read_Group_Flow_Order
parse_SAM_V1_6_Read_Group_FO = do
  ()
_ <- do ByteString
rgheaderflowordertagp <- (Word8 -> Bool) -> Parser ByteString
DABL.takeTill (Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
58)
          -- Parse FO tag of the header section.
          case (ByteString
rgheaderflowordertagp ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[F][O]|]) 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_Read_Group_Flow_Order_Incorrect_Format
            Bool
True  -> -- FO tag 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
  ByteString
rgheaderflowordervalue <- do ByteString
rgheaderflowordervaluep <- (Word8 -> Bool) -> Parser 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 FO value of the header section.
                               case (ByteString
rgheaderflowordervaluep ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|\*|[ACMGRSVTWYHKDBN]+|]) 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_Read_Group_Flow_Order_Incorrect_Format
                                 Bool
True  -> -- FO value is in the accepted format.
                                          ByteString -> Parser ByteString
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return ByteString
rgheaderflowordervaluep
  SAM_V1_6_Read_Group_Flow_Order
-> Parser SAM_V1_6_Read_Group_Flow_Order
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return SAM_V1_6_Read_Group_Flow_Order { sam_v1_6_read_group_flow_order_value :: ByteString
sam_v1_6_read_group_flow_order_value = ByteString
rgheaderflowordervalue
                                        }