{-# LANGUAGE FlexibleContexts      #-}
{-# LANGUAGE FlexibleInstances     #-}
{-# LANGUAGE MultiParamTypeClasses #-}
{-# LANGUAGE TypeFamilies          #-}

-- |
-- Module      :  Data.SAM.Version1_6.Read.Base
-- Copyright   :  (c) Matthew Mosior 2023
-- License     :  BSD-style
-- Maintainer  :  mattm.github@gmail.com
-- Portability :  portable
--
-- = Description
--
-- This library enables the decoding/encoding of SAM, BAM and CRAM file formats.

module Data.SAM.Version1_6.Read.Base ( -- * Reading
                                       readSAM_V1_6
                                     ) where

import Data.SAM.Version1_6.Base
import Data.SAM.Version1_6.Read.Parser.Header.HD.Base
import Data.SAM.Version1_6.Read.Parser.Header.SQ.Base
import Data.SAM.Version1_6.Read.Parser.Header.RG.Base
import Data.SAM.Version1_6.Read.Parser.Header.PG.Base
import Data.SAM.Version1_6.Read.Parser.Header.CO.Base
import Data.SAM.Version1_6.Read.Parser.Alignment.Base

import Control.Applicative.Permutations                          (intercalateEffect,toPermutationWithDefault)
import Data.Attoparsec.ByteString.Char8  as DABC8                (endOfLine)
import Data.Attoparsec.ByteString.Lazy   as DABL
import Data.ByteString.Lazy              as DBL
import Data.Sequence                     as DSeq
import qualified Streamly.Data.Stream    as S
import Streamly.External.ByteString.Lazy as StreamlyLByteString  (fromChunksIO)
import Streamly.Internal.FileSystem.File as StreamlyInternalFile (chunkReader)

-- | Make a parser optional, return Nothing if there is no match.
maybeOption :: Parser a
            -> Parser (Maybe a)
maybeOption p = option Nothing (Just <$> p)

-- | Define the @"SAM_V1_6"@ parser.
parse_SAM_V1_6 :: Parser SAM_V1_6
parse_SAM_V1_6 = do
  filelevelmetadata <- maybeOption parse_SAM_V1_6_File_Level_Metadata
  case filelevelmetadata of
    Nothing  -> do samwoalignment <- intercalateEffect endOfLine $
                                       (,,,)
                                         <$> toPermutationWithDefault Nothing
                                                                      (Just <$> DABL.many1' parse_SAM_V1_6_Reference_Sequence_Dictionary)
                                         <*> toPermutationWithDefault Nothing
                                                                      (Just <$> DABL.many1' parse_SAM_V1_6_Read_Group)
                                         <*> toPermutationWithDefault Nothing
                                                                      (Just <$> parse_SAM_V1_6_Program)
                                         <*> toPermutationWithDefault Nothing
                                                                      (Just <$> DABL.many1' parse_SAM_V1_6_One_Line_Comment)
                   alignment <- DABL.many1' parse_SAM_V1_6_Alignment
                   return SAM_V1_6 { sam_v1_6_file_level_metadata           = Nothing
                                   , sam_v1_6_reference_sequence_dictionary = (\(a,_,_,_) -> case a of
                                                                                               Nothing      -> Nothing
                                                                                               Just finala  -> Just $ DSeq.fromList finala
                                                                              ) samwoalignment
                                   , sam_v1_6_read_group                    = (\(_,b,_,_) -> case b of
                                                                                               Nothing      -> Nothing
                                                                                               Just finalb  -> Just $ DSeq.fromList finalb
                                                                              ) samwoalignment
                                   , sam_v1_6_program                       = (\(_,_,c,_) -> c) samwoalignment
                                   , sam_v1_6_one_line_comment              = (\(_,_,_,d) -> case d of
                                                                                               Nothing      -> Nothing
                                                                                               Just finald  -> Just $ DSeq.fromList finald
                                                                              ) samwoalignment
                                   , sam_v1_6_alignment                     = DSeq.fromList alignment
                                   }
    Just flm -> do samwoalignment <- intercalateEffect endOfLine $
                                       (,,,)
                                         <$> toPermutationWithDefault Nothing
                                                                      (Just <$> DABL.many1' parse_SAM_V1_6_Reference_Sequence_Dictionary)
                                         <*> toPermutationWithDefault Nothing
                                                                      (Just <$> DABL.many1' parse_SAM_V1_6_Read_Group)
                                         <*> toPermutationWithDefault Nothing
                                                                      (Just <$> parse_SAM_V1_6_Program)
                                         <*> toPermutationWithDefault Nothing
                                                                      (Just <$> DABL.many1' parse_SAM_V1_6_One_Line_Comment)
                   alignment <- DABL.many1' parse_SAM_V1_6_Alignment
                   return SAM_V1_6 { sam_v1_6_file_level_metadata           = Just flm
                                   , sam_v1_6_reference_sequence_dictionary = (\(a,_,_,_) -> case a of
                                                                                               Nothing      -> Nothing
                                                                                               Just finala  -> Just $ DSeq.fromList finala
                                                                              ) samwoalignment
                                   , sam_v1_6_read_group                    = (\(_,b,_,_) -> case b of
                                                                                               Nothing      -> Nothing
                                                                                               Just finalb  -> Just $ DSeq.fromList finalb
                                                                              ) samwoalignment
                                   , sam_v1_6_program                       = (\(_,_,c,_) -> c) samwoalignment
                                   , sam_v1_6_one_line_comment              = (\(_,_,_,d) -> case d of
                                                                                               Nothing      -> Nothing
                                                                                               Just finald  -> Just $ DSeq.fromList finald
                                                                              ) samwoalignment
                                   , sam_v1_6_alignment                     = DSeq.fromList alignment
                                   }

-- | Run the @"SAM_V1_6"@ parser.
readSAM_V1_6_LBS :: DBL.ByteString
                 -> IO SAM_V1_6
readSAM_V1_6_LBS lbs =
  case (DABL.parseOnly parse_SAM_V1_6 lbs) of 
    Left  samparseerror -> error samparseerror
    Right sam           -> return sam

-- | Read a @"SAM_V1_6"@ from a file.
--
-- The file is checked for errors as it is parsed.
--
-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.
readSAM_V1_6 :: FilePath -- ^ Input path to SAM file.
             -> IO SAM_V1_6
readSAM_V1_6 fp = do
  let lazysamfile = S.unfold StreamlyInternalFile.chunkReader fp
  lazysamfilef    <- StreamlyLByteString.fromChunksIO lazysamfile
  readSAM_V1_6_LBS lazysamfilef