Base.hs

{-# 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.SQ.Base
-- 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.SQ.Base ( -- * SAM_V1_6 parser - header section (Reference sequence dictionary)
                                                        parse_SAM_V1_6_Reference_Sequence_Dictionary
                                                      ) where

import Data.SAM.Version1_6.Header
import Data.SAM.Version1_6.Read.Error
import Data.SAM.Version1_6.Read.Parser.Header.SQ.SN
import Data.SAM.Version1_6.Read.Parser.Header.SQ.LN
import Data.SAM.Version1_6.Read.Parser.Header.SQ.AH
import Data.SAM.Version1_6.Read.Parser.Header.SQ.AN
import Data.SAM.Version1_6.Read.Parser.Header.SQ.AS
import Data.SAM.Version1_6.Read.Parser.Header.SQ.DS
import Data.SAM.Version1_6.Read.Parser.Header.SQ.M5
import Data.SAM.Version1_6.Read.Parser.Header.SQ.SP
import Data.SAM.Version1_6.Read.Parser.Header.SQ.TP
import Data.SAM.Version1_6.Read.Parser.Header.SQ.UR

import Control.Applicative.Permutations           (intercalateEffect,toPermutation,toPermutationWithDefault)
import Data.Attoparsec.ByteString.Char8  as DABC8 (endOfLine)
import Data.Attoparsec.ByteString.Lazy   as DABL
import Text.Regex.PCRE.Heavy

-- | @"SAM_V1_6_Reference_Sequence_Dictionary"@ parser.
--
-- Defines a parser for @SQ 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_Reference_Sequence_Dictionary :: Parser SAM_V1_6_Reference_Sequence_Dictionary
parse_SAM_V1_6_Reference_Sequence_Dictionary = do
  _         <- do sqheaderp <- DABL.takeTill (== 09)
                  -- Parse @SQ tag of the header section.
                  case (sqheaderp =~ [re|[@][S][Q]|]) of
                    False -> fail $ show SAM_V1_6_Error_File_Level_Metadata_Tag_Incorrect_Format
                    True  -> -- @SQ tag is in the accepted format.
                             return ()
  _         <- word8 09
  -- This parser assumes that the
  -- SN, LN, AH, AN, AS, DS, M5,
  -- SP, TP and UR tags can appear in any order.
  sq <- intercalateEffect (word8 09) $
          SAM_V1_6_Reference_Sequence_Dictionary
            <$> toPermutation parse_SAM_V1_6_Reference_Sequence_Dictionary_SN
            <*> toPermutation parse_SAM_V1_6_Reference_Sequence_Dictionary_LN
            <*> toPermutationWithDefault Nothing
                                         (Just <$> parse_SAM_V1_6_Reference_Sequence_Dictionary_AH)
            <*> toPermutationWithDefault Nothing
                                         (Just <$> parse_SAM_V1_6_Reference_Sequence_Dictionary_AN)
            <*> toPermutationWithDefault Nothing
                                         (Just <$> parse_SAM_V1_6_Reference_Sequence_Dictionary_AS)
            <*> toPermutationWithDefault Nothing
                                         (Just <$> parse_SAM_V1_6_Reference_Sequence_Dictionary_DS)
            <*> toPermutationWithDefault Nothing
                                         (Just <$> parse_SAM_V1_6_Reference_Sequence_Dictionary_M5)
            <*> toPermutationWithDefault Nothing
                                         (Just <$> parse_SAM_V1_6_Reference_Sequence_Dictionary_SP) 
            <*> toPermutationWithDefault Nothing
                                         (Just <$> parse_SAM_V1_6_Reference_Sequence_Dictionary_TP)
            <*> toPermutationWithDefault Nothing
                                         (Just <$> parse_SAM_V1_6_Reference_Sequence_Dictionary_UR)
  _ <- endOfLine
  return sq