{-# 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 :: forall a. Parser a -> Parser (Maybe a)
maybeOption Parser a
p = Maybe a
-> Parser ByteString (Maybe a) -> Parser ByteString (Maybe a)
forall (f :: * -> *) a. Alternative f => a -> f a -> f a
option Maybe a
forall a. Maybe a
Nothing (a -> Maybe a
forall a. a -> Maybe a
Just (a -> Maybe a) -> Parser a -> Parser ByteString (Maybe a)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser a
p)

-- | Define the @"SAM_V1_6"@ parser.
parse_SAM_V1_6 :: Parser SAM_V1_6
parse_SAM_V1_6 :: Parser SAM_V1_6
parse_SAM_V1_6 = do
  Maybe SAM_V1_6_File_Level_Metadata
filelevelmetadata <- Parser SAM_V1_6_File_Level_Metadata
-> Parser (Maybe SAM_V1_6_File_Level_Metadata)
forall a. Parser a -> Parser (Maybe a)
maybeOption Parser SAM_V1_6_File_Level_Metadata
parse_SAM_V1_6_File_Level_Metadata
  case Maybe SAM_V1_6_File_Level_Metadata
filelevelmetadata of
    Maybe SAM_V1_6_File_Level_Metadata
Nothing  -> do (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
 Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
 Maybe [SAM_V1_6_One_Line_Comment])
samwoalignment <- Parser ByteString ()
-> Permutation
     (Parser ByteString)
     (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
      Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
      Maybe [SAM_V1_6_One_Line_Comment])
-> Parser
     ByteString
     (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
      Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
      Maybe [SAM_V1_6_One_Line_Comment])
forall (m :: * -> *) b a.
Alternative m =>
m b -> Permutation m a -> m a
intercalateEffect Parser ByteString ()
endOfLine (Permutation
   (Parser ByteString)
   (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
    Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
    Maybe [SAM_V1_6_One_Line_Comment])
 -> Parser
      ByteString
      (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
       Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
       Maybe [SAM_V1_6_One_Line_Comment]))
-> Permutation
     (Parser ByteString)
     (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
      Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
      Maybe [SAM_V1_6_One_Line_Comment])
-> Parser
     ByteString
     (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
      Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
      Maybe [SAM_V1_6_One_Line_Comment])
forall a b. (a -> b) -> a -> b
$
                                       (,,,)
                                         (Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
 -> Maybe [SAM_V1_6_Read_Group]
 -> Maybe SAM_V1_6_Program
 -> Maybe [SAM_V1_6_One_Line_Comment]
 -> (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
     Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
     Maybe [SAM_V1_6_One_Line_Comment]))
-> Permutation
     (Parser ByteString)
     (Maybe [SAM_V1_6_Reference_Sequence_Dictionary])
-> Permutation
     (Parser ByteString)
     (Maybe [SAM_V1_6_Read_Group]
      -> Maybe SAM_V1_6_Program
      -> Maybe [SAM_V1_6_One_Line_Comment]
      -> (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
          Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
          Maybe [SAM_V1_6_One_Line_Comment]))
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
-> Parser
     ByteString (Maybe [SAM_V1_6_Reference_Sequence_Dictionary])
-> Permutation
     (Parser ByteString)
     (Maybe [SAM_V1_6_Reference_Sequence_Dictionary])
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
forall a. Maybe a
Nothing
                                                                      ([SAM_V1_6_Reference_Sequence_Dictionary]
-> Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
forall a. a -> Maybe a
Just ([SAM_V1_6_Reference_Sequence_Dictionary]
 -> Maybe [SAM_V1_6_Reference_Sequence_Dictionary])
-> Parser ByteString [SAM_V1_6_Reference_Sequence_Dictionary]
-> Parser
     ByteString (Maybe [SAM_V1_6_Reference_Sequence_Dictionary])
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Reference_Sequence_Dictionary
-> Parser ByteString [SAM_V1_6_Reference_Sequence_Dictionary]
forall (m :: * -> *) a. MonadPlus m => m a -> m [a]
DABL.many1' Parser ByteString SAM_V1_6_Reference_Sequence_Dictionary
parse_SAM_V1_6_Reference_Sequence_Dictionary)
                                         Permutation
  (Parser ByteString)
  (Maybe [SAM_V1_6_Read_Group]
   -> Maybe SAM_V1_6_Program
   -> Maybe [SAM_V1_6_One_Line_Comment]
   -> (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
       Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
       Maybe [SAM_V1_6_One_Line_Comment]))
-> Permutation (Parser ByteString) (Maybe [SAM_V1_6_Read_Group])
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Program
      -> Maybe [SAM_V1_6_One_Line_Comment]
      -> (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
          Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
          Maybe [SAM_V1_6_One_Line_Comment]))
forall a b.
Permutation (Parser ByteString) (a -> b)
-> Permutation (Parser ByteString) a
-> Permutation (Parser ByteString) b
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Maybe [SAM_V1_6_Read_Group]
-> Parser ByteString (Maybe [SAM_V1_6_Read_Group])
-> Permutation (Parser ByteString) (Maybe [SAM_V1_6_Read_Group])
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe [SAM_V1_6_Read_Group]
forall a. Maybe a
Nothing
                                                                      ([SAM_V1_6_Read_Group] -> Maybe [SAM_V1_6_Read_Group]
forall a. a -> Maybe a
Just ([SAM_V1_6_Read_Group] -> Maybe [SAM_V1_6_Read_Group])
-> Parser ByteString [SAM_V1_6_Read_Group]
-> Parser ByteString (Maybe [SAM_V1_6_Read_Group])
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Read_Group
-> Parser ByteString [SAM_V1_6_Read_Group]
forall (m :: * -> *) a. MonadPlus m => m a -> m [a]
DABL.many1' Parser ByteString SAM_V1_6_Read_Group
parse_SAM_V1_6_Read_Group)
                                         Permutation
  (Parser ByteString)
  (Maybe SAM_V1_6_Program
   -> Maybe [SAM_V1_6_One_Line_Comment]
   -> (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
       Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
       Maybe [SAM_V1_6_One_Line_Comment]))
-> Permutation (Parser ByteString) (Maybe SAM_V1_6_Program)
-> Permutation
     (Parser ByteString)
     (Maybe [SAM_V1_6_One_Line_Comment]
      -> (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
          Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
          Maybe [SAM_V1_6_One_Line_Comment]))
forall a b.
Permutation (Parser ByteString) (a -> b)
-> Permutation (Parser ByteString) a
-> Permutation (Parser ByteString) b
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Maybe SAM_V1_6_Program
-> Parser ByteString (Maybe SAM_V1_6_Program)
-> Permutation (Parser ByteString) (Maybe SAM_V1_6_Program)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Program
forall a. Maybe a
Nothing
                                                                      (SAM_V1_6_Program -> Maybe SAM_V1_6_Program
forall a. a -> Maybe a
Just (SAM_V1_6_Program -> Maybe SAM_V1_6_Program)
-> Parser ByteString SAM_V1_6_Program
-> Parser ByteString (Maybe SAM_V1_6_Program)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Program
parse_SAM_V1_6_Program)
                                         Permutation
  (Parser ByteString)
  (Maybe [SAM_V1_6_One_Line_Comment]
   -> (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
       Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
       Maybe [SAM_V1_6_One_Line_Comment]))
-> Permutation
     (Parser ByteString) (Maybe [SAM_V1_6_One_Line_Comment])
-> Permutation
     (Parser ByteString)
     (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
      Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
      Maybe [SAM_V1_6_One_Line_Comment])
forall a b.
Permutation (Parser ByteString) (a -> b)
-> Permutation (Parser ByteString) a
-> Permutation (Parser ByteString) b
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Maybe [SAM_V1_6_One_Line_Comment]
-> Parser ByteString (Maybe [SAM_V1_6_One_Line_Comment])
-> Permutation
     (Parser ByteString) (Maybe [SAM_V1_6_One_Line_Comment])
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe [SAM_V1_6_One_Line_Comment]
forall a. Maybe a
Nothing
                                                                      ([SAM_V1_6_One_Line_Comment] -> Maybe [SAM_V1_6_One_Line_Comment]
forall a. a -> Maybe a
Just ([SAM_V1_6_One_Line_Comment] -> Maybe [SAM_V1_6_One_Line_Comment])
-> Parser ByteString [SAM_V1_6_One_Line_Comment]
-> Parser ByteString (Maybe [SAM_V1_6_One_Line_Comment])
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_One_Line_Comment
-> Parser ByteString [SAM_V1_6_One_Line_Comment]
forall (m :: * -> *) a. MonadPlus m => m a -> m [a]
DABL.many1' Parser ByteString SAM_V1_6_One_Line_Comment
parse_SAM_V1_6_One_Line_Comment)
                   [SAM_V1_6_Alignment]
alignment <- Parser ByteString SAM_V1_6_Alignment
-> Parser ByteString [SAM_V1_6_Alignment]
forall (m :: * -> *) a. MonadPlus m => m a -> m [a]
DABL.many1' Parser ByteString SAM_V1_6_Alignment
parse_SAM_V1_6_Alignment
                   SAM_V1_6 -> Parser SAM_V1_6
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return SAM_V1_6 { sam_v1_6_file_level_metadata :: Maybe SAM_V1_6_File_Level_Metadata
sam_v1_6_file_level_metadata           = Maybe SAM_V1_6_File_Level_Metadata
forall a. Maybe a
Nothing
                                   , sam_v1_6_reference_sequence_dictionary :: Maybe (Seq SAM_V1_6_Reference_Sequence_Dictionary)
sam_v1_6_reference_sequence_dictionary = (\(Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
a,Maybe [SAM_V1_6_Read_Group]
_,Maybe SAM_V1_6_Program
_,Maybe [SAM_V1_6_One_Line_Comment]
_) -> case Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
a of
                                                                                               Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
Nothing      -> Maybe (Seq SAM_V1_6_Reference_Sequence_Dictionary)
forall a. Maybe a
Nothing
                                                                                               Just [SAM_V1_6_Reference_Sequence_Dictionary]
finala  -> Seq SAM_V1_6_Reference_Sequence_Dictionary
-> Maybe (Seq SAM_V1_6_Reference_Sequence_Dictionary)
forall a. a -> Maybe a
Just (Seq SAM_V1_6_Reference_Sequence_Dictionary
 -> Maybe (Seq SAM_V1_6_Reference_Sequence_Dictionary))
-> Seq SAM_V1_6_Reference_Sequence_Dictionary
-> Maybe (Seq SAM_V1_6_Reference_Sequence_Dictionary)
forall a b. (a -> b) -> a -> b
$ [SAM_V1_6_Reference_Sequence_Dictionary]
-> Seq SAM_V1_6_Reference_Sequence_Dictionary
forall a. [a] -> Seq a
DSeq.fromList [SAM_V1_6_Reference_Sequence_Dictionary]
finala
                                                                              ) (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
 Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
 Maybe [SAM_V1_6_One_Line_Comment])
samwoalignment
                                   , sam_v1_6_read_group :: Maybe (Seq SAM_V1_6_Read_Group)
sam_v1_6_read_group                    = (\(Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
_,Maybe [SAM_V1_6_Read_Group]
b,Maybe SAM_V1_6_Program
_,Maybe [SAM_V1_6_One_Line_Comment]
_) -> case Maybe [SAM_V1_6_Read_Group]
b of
                                                                                               Maybe [SAM_V1_6_Read_Group]
Nothing      -> Maybe (Seq SAM_V1_6_Read_Group)
forall a. Maybe a
Nothing
                                                                                               Just [SAM_V1_6_Read_Group]
finalb  -> Seq SAM_V1_6_Read_Group -> Maybe (Seq SAM_V1_6_Read_Group)
forall a. a -> Maybe a
Just (Seq SAM_V1_6_Read_Group -> Maybe (Seq SAM_V1_6_Read_Group))
-> Seq SAM_V1_6_Read_Group -> Maybe (Seq SAM_V1_6_Read_Group)
forall a b. (a -> b) -> a -> b
$ [SAM_V1_6_Read_Group] -> Seq SAM_V1_6_Read_Group
forall a. [a] -> Seq a
DSeq.fromList [SAM_V1_6_Read_Group]
finalb
                                                                              ) (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
 Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
 Maybe [SAM_V1_6_One_Line_Comment])
samwoalignment
                                   , sam_v1_6_program :: Maybe SAM_V1_6_Program
sam_v1_6_program                       = (\(Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
_,Maybe [SAM_V1_6_Read_Group]
_,Maybe SAM_V1_6_Program
c,Maybe [SAM_V1_6_One_Line_Comment]
_) -> Maybe SAM_V1_6_Program
c) (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
 Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
 Maybe [SAM_V1_6_One_Line_Comment])
samwoalignment
                                   , sam_v1_6_one_line_comment :: Maybe (Seq SAM_V1_6_One_Line_Comment)
sam_v1_6_one_line_comment              = (\(Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
_,Maybe [SAM_V1_6_Read_Group]
_,Maybe SAM_V1_6_Program
_,Maybe [SAM_V1_6_One_Line_Comment]
d) -> case Maybe [SAM_V1_6_One_Line_Comment]
d of
                                                                                               Maybe [SAM_V1_6_One_Line_Comment]
Nothing      -> Maybe (Seq SAM_V1_6_One_Line_Comment)
forall a. Maybe a
Nothing
                                                                                               Just [SAM_V1_6_One_Line_Comment]
finald  -> Seq SAM_V1_6_One_Line_Comment
-> Maybe (Seq SAM_V1_6_One_Line_Comment)
forall a. a -> Maybe a
Just (Seq SAM_V1_6_One_Line_Comment
 -> Maybe (Seq SAM_V1_6_One_Line_Comment))
-> Seq SAM_V1_6_One_Line_Comment
-> Maybe (Seq SAM_V1_6_One_Line_Comment)
forall a b. (a -> b) -> a -> b
$ [SAM_V1_6_One_Line_Comment] -> Seq SAM_V1_6_One_Line_Comment
forall a. [a] -> Seq a
DSeq.fromList [SAM_V1_6_One_Line_Comment]
finald
                                                                              ) (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
 Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
 Maybe [SAM_V1_6_One_Line_Comment])
samwoalignment
                                   , sam_v1_6_alignment :: Seq SAM_V1_6_Alignment
sam_v1_6_alignment                     = [SAM_V1_6_Alignment] -> Seq SAM_V1_6_Alignment
forall a. [a] -> Seq a
DSeq.fromList [SAM_V1_6_Alignment]
alignment
                                   }
    Just SAM_V1_6_File_Level_Metadata
flm -> do (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
 Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
 Maybe [SAM_V1_6_One_Line_Comment])
samwoalignment <- Parser ByteString ()
-> Permutation
     (Parser ByteString)
     (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
      Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
      Maybe [SAM_V1_6_One_Line_Comment])
-> Parser
     ByteString
     (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
      Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
      Maybe [SAM_V1_6_One_Line_Comment])
forall (m :: * -> *) b a.
Alternative m =>
m b -> Permutation m a -> m a
intercalateEffect Parser ByteString ()
endOfLine (Permutation
   (Parser ByteString)
   (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
    Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
    Maybe [SAM_V1_6_One_Line_Comment])
 -> Parser
      ByteString
      (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
       Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
       Maybe [SAM_V1_6_One_Line_Comment]))
-> Permutation
     (Parser ByteString)
     (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
      Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
      Maybe [SAM_V1_6_One_Line_Comment])
-> Parser
     ByteString
     (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
      Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
      Maybe [SAM_V1_6_One_Line_Comment])
forall a b. (a -> b) -> a -> b
$
                                       (,,,)
                                         (Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
 -> Maybe [SAM_V1_6_Read_Group]
 -> Maybe SAM_V1_6_Program
 -> Maybe [SAM_V1_6_One_Line_Comment]
 -> (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
     Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
     Maybe [SAM_V1_6_One_Line_Comment]))
-> Permutation
     (Parser ByteString)
     (Maybe [SAM_V1_6_Reference_Sequence_Dictionary])
-> Permutation
     (Parser ByteString)
     (Maybe [SAM_V1_6_Read_Group]
      -> Maybe SAM_V1_6_Program
      -> Maybe [SAM_V1_6_One_Line_Comment]
      -> (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
          Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
          Maybe [SAM_V1_6_One_Line_Comment]))
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
-> Parser
     ByteString (Maybe [SAM_V1_6_Reference_Sequence_Dictionary])
-> Permutation
     (Parser ByteString)
     (Maybe [SAM_V1_6_Reference_Sequence_Dictionary])
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
forall a. Maybe a
Nothing
                                                                      ([SAM_V1_6_Reference_Sequence_Dictionary]
-> Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
forall a. a -> Maybe a
Just ([SAM_V1_6_Reference_Sequence_Dictionary]
 -> Maybe [SAM_V1_6_Reference_Sequence_Dictionary])
-> Parser ByteString [SAM_V1_6_Reference_Sequence_Dictionary]
-> Parser
     ByteString (Maybe [SAM_V1_6_Reference_Sequence_Dictionary])
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Reference_Sequence_Dictionary
-> Parser ByteString [SAM_V1_6_Reference_Sequence_Dictionary]
forall (m :: * -> *) a. MonadPlus m => m a -> m [a]
DABL.many1' Parser ByteString SAM_V1_6_Reference_Sequence_Dictionary
parse_SAM_V1_6_Reference_Sequence_Dictionary)
                                         Permutation
  (Parser ByteString)
  (Maybe [SAM_V1_6_Read_Group]
   -> Maybe SAM_V1_6_Program
   -> Maybe [SAM_V1_6_One_Line_Comment]
   -> (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
       Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
       Maybe [SAM_V1_6_One_Line_Comment]))
-> Permutation (Parser ByteString) (Maybe [SAM_V1_6_Read_Group])
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Program
      -> Maybe [SAM_V1_6_One_Line_Comment]
      -> (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
          Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
          Maybe [SAM_V1_6_One_Line_Comment]))
forall a b.
Permutation (Parser ByteString) (a -> b)
-> Permutation (Parser ByteString) a
-> Permutation (Parser ByteString) b
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Maybe [SAM_V1_6_Read_Group]
-> Parser ByteString (Maybe [SAM_V1_6_Read_Group])
-> Permutation (Parser ByteString) (Maybe [SAM_V1_6_Read_Group])
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe [SAM_V1_6_Read_Group]
forall a. Maybe a
Nothing
                                                                      ([SAM_V1_6_Read_Group] -> Maybe [SAM_V1_6_Read_Group]
forall a. a -> Maybe a
Just ([SAM_V1_6_Read_Group] -> Maybe [SAM_V1_6_Read_Group])
-> Parser ByteString [SAM_V1_6_Read_Group]
-> Parser ByteString (Maybe [SAM_V1_6_Read_Group])
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Read_Group
-> Parser ByteString [SAM_V1_6_Read_Group]
forall (m :: * -> *) a. MonadPlus m => m a -> m [a]
DABL.many1' Parser ByteString SAM_V1_6_Read_Group
parse_SAM_V1_6_Read_Group)
                                         Permutation
  (Parser ByteString)
  (Maybe SAM_V1_6_Program
   -> Maybe [SAM_V1_6_One_Line_Comment]
   -> (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
       Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
       Maybe [SAM_V1_6_One_Line_Comment]))
-> Permutation (Parser ByteString) (Maybe SAM_V1_6_Program)
-> Permutation
     (Parser ByteString)
     (Maybe [SAM_V1_6_One_Line_Comment]
      -> (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
          Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
          Maybe [SAM_V1_6_One_Line_Comment]))
forall a b.
Permutation (Parser ByteString) (a -> b)
-> Permutation (Parser ByteString) a
-> Permutation (Parser ByteString) b
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Maybe SAM_V1_6_Program
-> Parser ByteString (Maybe SAM_V1_6_Program)
-> Permutation (Parser ByteString) (Maybe SAM_V1_6_Program)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Program
forall a. Maybe a
Nothing
                                                                      (SAM_V1_6_Program -> Maybe SAM_V1_6_Program
forall a. a -> Maybe a
Just (SAM_V1_6_Program -> Maybe SAM_V1_6_Program)
-> Parser ByteString SAM_V1_6_Program
-> Parser ByteString (Maybe SAM_V1_6_Program)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Program
parse_SAM_V1_6_Program)
                                         Permutation
  (Parser ByteString)
  (Maybe [SAM_V1_6_One_Line_Comment]
   -> (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
       Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
       Maybe [SAM_V1_6_One_Line_Comment]))
-> Permutation
     (Parser ByteString) (Maybe [SAM_V1_6_One_Line_Comment])
-> Permutation
     (Parser ByteString)
     (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
      Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
      Maybe [SAM_V1_6_One_Line_Comment])
forall a b.
Permutation (Parser ByteString) (a -> b)
-> Permutation (Parser ByteString) a
-> Permutation (Parser ByteString) b
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Maybe [SAM_V1_6_One_Line_Comment]
-> Parser ByteString (Maybe [SAM_V1_6_One_Line_Comment])
-> Permutation
     (Parser ByteString) (Maybe [SAM_V1_6_One_Line_Comment])
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe [SAM_V1_6_One_Line_Comment]
forall a. Maybe a
Nothing
                                                                      ([SAM_V1_6_One_Line_Comment] -> Maybe [SAM_V1_6_One_Line_Comment]
forall a. a -> Maybe a
Just ([SAM_V1_6_One_Line_Comment] -> Maybe [SAM_V1_6_One_Line_Comment])
-> Parser ByteString [SAM_V1_6_One_Line_Comment]
-> Parser ByteString (Maybe [SAM_V1_6_One_Line_Comment])
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_One_Line_Comment
-> Parser ByteString [SAM_V1_6_One_Line_Comment]
forall (m :: * -> *) a. MonadPlus m => m a -> m [a]
DABL.many1' Parser ByteString SAM_V1_6_One_Line_Comment
parse_SAM_V1_6_One_Line_Comment)
                   [SAM_V1_6_Alignment]
alignment <- Parser ByteString SAM_V1_6_Alignment
-> Parser ByteString [SAM_V1_6_Alignment]
forall (m :: * -> *) a. MonadPlus m => m a -> m [a]
DABL.many1' Parser ByteString SAM_V1_6_Alignment
parse_SAM_V1_6_Alignment
                   SAM_V1_6 -> Parser SAM_V1_6
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return SAM_V1_6 { sam_v1_6_file_level_metadata :: Maybe SAM_V1_6_File_Level_Metadata
sam_v1_6_file_level_metadata           = SAM_V1_6_File_Level_Metadata -> Maybe SAM_V1_6_File_Level_Metadata
forall a. a -> Maybe a
Just SAM_V1_6_File_Level_Metadata
flm
                                   , sam_v1_6_reference_sequence_dictionary :: Maybe (Seq SAM_V1_6_Reference_Sequence_Dictionary)
sam_v1_6_reference_sequence_dictionary = (\(Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
a,Maybe [SAM_V1_6_Read_Group]
_,Maybe SAM_V1_6_Program
_,Maybe [SAM_V1_6_One_Line_Comment]
_) -> case Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
a of
                                                                                               Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
Nothing      -> Maybe (Seq SAM_V1_6_Reference_Sequence_Dictionary)
forall a. Maybe a
Nothing
                                                                                               Just [SAM_V1_6_Reference_Sequence_Dictionary]
finala  -> Seq SAM_V1_6_Reference_Sequence_Dictionary
-> Maybe (Seq SAM_V1_6_Reference_Sequence_Dictionary)
forall a. a -> Maybe a
Just (Seq SAM_V1_6_Reference_Sequence_Dictionary
 -> Maybe (Seq SAM_V1_6_Reference_Sequence_Dictionary))
-> Seq SAM_V1_6_Reference_Sequence_Dictionary
-> Maybe (Seq SAM_V1_6_Reference_Sequence_Dictionary)
forall a b. (a -> b) -> a -> b
$ [SAM_V1_6_Reference_Sequence_Dictionary]
-> Seq SAM_V1_6_Reference_Sequence_Dictionary
forall a. [a] -> Seq a
DSeq.fromList [SAM_V1_6_Reference_Sequence_Dictionary]
finala
                                                                              ) (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
 Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
 Maybe [SAM_V1_6_One_Line_Comment])
samwoalignment
                                   , sam_v1_6_read_group :: Maybe (Seq SAM_V1_6_Read_Group)
sam_v1_6_read_group                    = (\(Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
_,Maybe [SAM_V1_6_Read_Group]
b,Maybe SAM_V1_6_Program
_,Maybe [SAM_V1_6_One_Line_Comment]
_) -> case Maybe [SAM_V1_6_Read_Group]
b of
                                                                                               Maybe [SAM_V1_6_Read_Group]
Nothing      -> Maybe (Seq SAM_V1_6_Read_Group)
forall a. Maybe a
Nothing
                                                                                               Just [SAM_V1_6_Read_Group]
finalb  -> Seq SAM_V1_6_Read_Group -> Maybe (Seq SAM_V1_6_Read_Group)
forall a. a -> Maybe a
Just (Seq SAM_V1_6_Read_Group -> Maybe (Seq SAM_V1_6_Read_Group))
-> Seq SAM_V1_6_Read_Group -> Maybe (Seq SAM_V1_6_Read_Group)
forall a b. (a -> b) -> a -> b
$ [SAM_V1_6_Read_Group] -> Seq SAM_V1_6_Read_Group
forall a. [a] -> Seq a
DSeq.fromList [SAM_V1_6_Read_Group]
finalb
                                                                              ) (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
 Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
 Maybe [SAM_V1_6_One_Line_Comment])
samwoalignment
                                   , sam_v1_6_program :: Maybe SAM_V1_6_Program
sam_v1_6_program                       = (\(Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
_,Maybe [SAM_V1_6_Read_Group]
_,Maybe SAM_V1_6_Program
c,Maybe [SAM_V1_6_One_Line_Comment]
_) -> Maybe SAM_V1_6_Program
c) (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
 Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
 Maybe [SAM_V1_6_One_Line_Comment])
samwoalignment
                                   , sam_v1_6_one_line_comment :: Maybe (Seq SAM_V1_6_One_Line_Comment)
sam_v1_6_one_line_comment              = (\(Maybe [SAM_V1_6_Reference_Sequence_Dictionary]
_,Maybe [SAM_V1_6_Read_Group]
_,Maybe SAM_V1_6_Program
_,Maybe [SAM_V1_6_One_Line_Comment]
d) -> case Maybe [SAM_V1_6_One_Line_Comment]
d of
                                                                                               Maybe [SAM_V1_6_One_Line_Comment]
Nothing      -> Maybe (Seq SAM_V1_6_One_Line_Comment)
forall a. Maybe a
Nothing
                                                                                               Just [SAM_V1_6_One_Line_Comment]
finald  -> Seq SAM_V1_6_One_Line_Comment
-> Maybe (Seq SAM_V1_6_One_Line_Comment)
forall a. a -> Maybe a
Just (Seq SAM_V1_6_One_Line_Comment
 -> Maybe (Seq SAM_V1_6_One_Line_Comment))
-> Seq SAM_V1_6_One_Line_Comment
-> Maybe (Seq SAM_V1_6_One_Line_Comment)
forall a b. (a -> b) -> a -> b
$ [SAM_V1_6_One_Line_Comment] -> Seq SAM_V1_6_One_Line_Comment
forall a. [a] -> Seq a
DSeq.fromList [SAM_V1_6_One_Line_Comment]
finald
                                                                              ) (Maybe [SAM_V1_6_Reference_Sequence_Dictionary],
 Maybe [SAM_V1_6_Read_Group], Maybe SAM_V1_6_Program,
 Maybe [SAM_V1_6_One_Line_Comment])
samwoalignment
                                   , sam_v1_6_alignment :: Seq SAM_V1_6_Alignment
sam_v1_6_alignment                     = [SAM_V1_6_Alignment] -> Seq SAM_V1_6_Alignment
forall a. [a] -> Seq a
DSeq.fromList [SAM_V1_6_Alignment]
alignment
                                   }

-- | Run the @"SAM_V1_6"@ parser.
readSAM_V1_6_LBS :: DBL.ByteString
                 -> IO SAM_V1_6
readSAM_V1_6_LBS :: ByteString -> IO SAM_V1_6
readSAM_V1_6_LBS ByteString
lbs =
  case (Parser SAM_V1_6 -> ByteString -> Either String SAM_V1_6
forall a. Parser a -> ByteString -> Either String a
DABL.parseOnly Parser SAM_V1_6
parse_SAM_V1_6 ByteString
lbs) of 
    Left  String
samparseerror -> String -> IO SAM_V1_6
forall a. HasCallStack => String -> a
error String
samparseerror
    Right SAM_V1_6
sam           -> SAM_V1_6 -> IO SAM_V1_6
forall a. a -> IO a
forall (m :: * -> *) a. Monad m => a -> m a
return SAM_V1_6
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 :: String -> IO SAM_V1_6
readSAM_V1_6 String
fp = do
  let lazysamfile :: Stream IO (Array Word8)
lazysamfile = Unfold IO String (Array Word8) -> String -> Stream IO (Array Word8)
forall (m :: * -> *) a b.
Applicative m =>
Unfold m a b -> a -> Stream m b
S.unfold Unfold IO String (Array Word8)
forall (m :: * -> *).
(MonadIO m, MonadCatch m) =>
Unfold m String (Array Word8)
StreamlyInternalFile.chunkReader String
fp
  ByteString
lazysamfilef    <- Stream IO (Array Word8) -> IO ByteString
StreamlyLByteString.fromChunksIO Stream IO (Array Word8)
lazysamfile
  ByteString -> IO SAM_V1_6
readSAM_V1_6_LBS ByteString
lazysamfilef