GO.hs

{-# 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.GO
-- 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.GO ( -- * SAM_V1_6 parser - header section (File-level metadata) - GO tag
                                                      parse_SAM_V1_6_File_Level_Metadata_GO
                                                    ) 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 GO 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_GO :: Parser SAM_V1_6_File_Level_Metadata_Alignment_Grouping
parse_SAM_V1_6_File_Level_Metadata_GO = do
  hdheaderalignmentgroupingtag <- do hdheaderalignmentgroupingtagp <- DABL.takeTill (== 58)
                                     -- Parse GO tag of the header section.
                                     case (hdheaderalignmentgroupingtagp =~ [re|[G][O]|]) of
                                       False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Grouping_Of_Alignments_Tag_Incorrect_Format
                                       True  -> -- GO tag is in the accepted format.
                                                return hdheaderalignmentgroupingtagp
  _ <- word8 58
  hdheaderalignmentgroupingvalue <- do hdheaderalignmentgroupingvaluep <- DABL.takeTill (== 09)
                                       -- Parse GO value of the header section.
                                       case (hdheaderalignmentgroupingvaluep =~ [re|[n][o][n][e]|[q][u][e][r][y]|[r][e][f][e][r][e][n][c][e]|]) of
                                         False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Grouping_Of_Alignments_Invalid_Value
                                         True  -> -- GO value is in the accepted format.
                                                  return hdheaderalignmentgroupingvaluep
  return SAM_V1_6_File_Level_Metadata_Alignment_Grouping { sam_v1_6_file_level_metadata_alignment_grouping_tag   = DSeq.fromList $ DB.unpack hdheaderalignmentgroupingtag
                                                         , sam_v1_6_file_level_metadata_alignment_grouping_value = hdheaderalignmentgroupingvalue
                                                         }