{-# 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.Header.HD.SS
-- 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.HD.SS ( -- * SAM_V1_6 parser - header section (File-level metadata) - SS tag
                                                      parse_SAM_V1_6_File_Level_Metadata_SS
                                                    ) where

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

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

-- | Defines a parser for the SS tag of the @HD 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_File_Level_Metadata_SS :: Parser SAM_V1_6_File_Level_Metadata_SubSorting_Order
parse_SAM_V1_6_File_Level_Metadata_SS :: Parser SAM_V1_6_File_Level_Metadata_SubSorting_Order
parse_SAM_V1_6_File_Level_Metadata_SS = do
  ByteString
hdheadersubsortingordertag <- do ByteString
hdheadersubsortingordertagp <- (Word8 -> Bool) -> Parser ByteString ByteString
DABL.takeTill (Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
58)
                                   -- Parse SS tag of the header section.
                                   case (ByteString
hdheadersubsortingordertagp ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[S][S]|]) 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_File_Level_Metadata_Subsorting_Order_Tag_Incorrect_Format
                                     Bool
True  -> -- SS 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
hdheadersubsortingordertagp
  Word8
_ <- Word8 -> Parser Word8
word8 Word8
58
  ByteString
hdheadersubsortingordervalue <- do ByteString
hdheadersubsortingordervaluep <- (Word8 -> Bool) -> Parser ByteString ByteString
DABL.takeTill (Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
09)
                                     -- Parse SS value of the header section.
                                     case (ByteString
hdheadersubsortingordervaluep ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|(coordinate|queryname|unsorted)(:[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_File_Level_Metadata_Subsorting_Order_Incorrect_Format 
                                       Bool
True  -> -- SS 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
hdheadersubsortingordervaluep 
  SAM_V1_6_File_Level_Metadata_SubSorting_Order
-> Parser SAM_V1_6_File_Level_Metadata_SubSorting_Order
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return SAM_V1_6_File_Level_Metadata_SubSorting_Order { sam_v1_6_file_level_metadata_subsorting_order_tag :: Seq Word8
sam_v1_6_file_level_metadata_subsorting_order_tag   = [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
hdheadersubsortingordertag
                                                       , sam_v1_6_file_level_metadata_subsorting_order_value :: ByteString
sam_v1_6_file_level_metadata_subsorting_order_value = ByteString
hdheadersubsortingordervalue
                                                       }