{-# 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 :: Parser SAM_V1_6_Reference_Sequence_Dictionary
parse_SAM_V1_6_Reference_Sequence_Dictionary = do
  ()
_         <- do ByteString
sqheaderp <- (Word8 -> Bool) -> Parser ByteString
DABL.takeTill (Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
09)
                  -- Parse @SQ tag of the header section.
                  case (ByteString
sqheaderp ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[@][S][Q]|]) of
                    Bool
False -> String -> Parser ByteString ()
forall a. String -> Parser ByteString a
forall (m :: * -> *) a. MonadFail m => String -> m a
fail (String -> Parser ByteString ()) -> String -> Parser 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_Tag_Incorrect_Format
                    Bool
True  -> -- @SQ tag is in the accepted format.
                             () -> Parser ByteString ()
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return ()
  Word8
_         <- Word8 -> Parser Word8
word8 Word8
09
  -- This parser assumes that the
  -- SN, LN, AH, AN, AS, DS, M5,
  -- SP, TP and UR tags can appear in any order.
  SAM_V1_6_Reference_Sequence_Dictionary
sq <- Parser Word8
-> Permutation
     (Parser ByteString) SAM_V1_6_Reference_Sequence_Dictionary
-> Parser SAM_V1_6_Reference_Sequence_Dictionary
forall (m :: * -> *) b a.
Alternative m =>
m b -> Permutation m a -> m a
intercalateEffect (Word8 -> Parser Word8
word8 Word8
09) (Permutation
   (Parser ByteString) SAM_V1_6_Reference_Sequence_Dictionary
 -> Parser SAM_V1_6_Reference_Sequence_Dictionary)
-> Permutation
     (Parser ByteString) SAM_V1_6_Reference_Sequence_Dictionary
-> Parser SAM_V1_6_Reference_Sequence_Dictionary
forall a b. (a -> b) -> a -> b
$
          SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name
-> SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length
-> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus
-> Maybe
     SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names
-> Maybe
     SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier
-> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description
-> Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
-> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
-> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
-> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
-> SAM_V1_6_Reference_Sequence_Dictionary
SAM_V1_6_Reference_Sequence_Dictionary
            (SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name
 -> SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length
 -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus
 -> Maybe
      SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names
 -> Maybe
      SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier
 -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description
 -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
 -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
 -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
 -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
 -> SAM_V1_6_Reference_Sequence_Dictionary)
-> Permutation
     (Parser ByteString)
     SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name
-> Permutation
     (Parser ByteString)
     (SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus
      -> Maybe
           SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names
      -> Maybe
           SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
      -> 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_Reference_Sequence_Name
-> Permutation
     (Parser ByteString)
     SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name
forall (m :: * -> *) a. Alternative m => m a -> Permutation m a
toPermutation Parser
  ByteString
  SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name
parse_SAM_V1_6_Reference_Sequence_Dictionary_SN
            Permutation
  (Parser ByteString)
  (SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus
   -> Maybe
        SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names
   -> Maybe
        SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
   -> SAM_V1_6_Reference_Sequence_Dictionary)
-> Permutation
     (Parser ByteString)
     SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus
      -> Maybe
           SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names
      -> Maybe
           SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
      -> SAM_V1_6_Reference_Sequence_Dictionary)
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
<*> Parser
  ByteString
  SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length
-> Permutation
     (Parser ByteString)
     SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length
forall (m :: * -> *) a. Alternative m => m a -> Permutation m a
toPermutation Parser
  ByteString
  SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length
parse_SAM_V1_6_Reference_Sequence_Dictionary_LN
            Permutation
  (Parser ByteString)
  (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus
   -> Maybe
        SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names
   -> Maybe
        SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
   -> SAM_V1_6_Reference_Sequence_Dictionary)
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus)
-> Permutation
     (Parser ByteString)
     (Maybe
        SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names
      -> Maybe
           SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
      -> SAM_V1_6_Reference_Sequence_Dictionary)
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_Reference_Sequence_Dictionary_Alternative_Locus
-> Parser
     ByteString
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus)
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus
forall a. Maybe a
Nothing
                                         (SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus
-> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus
forall a. a -> Maybe a
Just (SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus
 -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus)
-> Parser
     ByteString SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus
-> Parser
     ByteString
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser
  ByteString SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus
parse_SAM_V1_6_Reference_Sequence_Dictionary_AH)
            Permutation
  (Parser ByteString)
  (Maybe
     SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names
   -> Maybe
        SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
   -> SAM_V1_6_Reference_Sequence_Dictionary)
-> Permutation
     (Parser ByteString)
     (Maybe
        SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names)
-> Permutation
     (Parser ByteString)
     (Maybe
        SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
      -> SAM_V1_6_Reference_Sequence_Dictionary)
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_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names
-> Parser
     ByteString
     (Maybe
        SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names)
-> Permutation
     (Parser ByteString)
     (Maybe
        SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe
  SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names
forall a. Maybe a
Nothing
                                         (SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names
-> Maybe
     SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names
forall a. a -> Maybe a
Just (SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names
 -> Maybe
      SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names)
-> Parser
     ByteString
     SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names
-> Parser
     ByteString
     (Maybe
        SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser
  ByteString
  SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names
parse_SAM_V1_6_Reference_Sequence_Dictionary_AN)
            Permutation
  (Parser ByteString)
  (Maybe
     SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
   -> SAM_V1_6_Reference_Sequence_Dictionary)
-> Permutation
     (Parser ByteString)
     (Maybe
        SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier)
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
      -> SAM_V1_6_Reference_Sequence_Dictionary)
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_Reference_Sequence_Dictionary_Genome_Assembly_Identifier
-> Parser
     ByteString
     (Maybe
        SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier)
-> Permutation
     (Parser ByteString)
     (Maybe
        SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe
  SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier
forall a. Maybe a
Nothing
                                         (SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier
-> Maybe
     SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier
forall a. a -> Maybe a
Just (SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier
 -> Maybe
      SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier)
-> Parser
     ByteString
     SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier
-> Parser
     ByteString
     (Maybe
        SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser
  ByteString
  SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier
parse_SAM_V1_6_Reference_Sequence_Dictionary_AS)
            Permutation
  (Parser ByteString)
  (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
   -> SAM_V1_6_Reference_Sequence_Dictionary)
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description)
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
      -> SAM_V1_6_Reference_Sequence_Dictionary)
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_Reference_Sequence_Dictionary_Description
-> Parser
     ByteString
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description)
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description
forall a. Maybe a
Nothing
                                         (SAM_V1_6_Reference_Sequence_Dictionary_Description
-> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description
forall a. a -> Maybe a
Just (SAM_V1_6_Reference_Sequence_Dictionary_Description
 -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description)
-> Parser
     ByteString SAM_V1_6_Reference_Sequence_Dictionary_Description
-> Parser
     ByteString
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser
  ByteString SAM_V1_6_Reference_Sequence_Dictionary_Description
parse_SAM_V1_6_Reference_Sequence_Dictionary_DS)
            Permutation
  (Parser ByteString)
  (Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
   -> SAM_V1_6_Reference_Sequence_Dictionary)
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum)
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
      -> SAM_V1_6_Reference_Sequence_Dictionary)
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_Reference_Sequence_Dictionary_MD5_Checksum
-> Parser
     ByteString
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum)
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
forall a. Maybe a
Nothing
                                         (SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
-> Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
forall a. a -> Maybe a
Just (SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
 -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum)
-> Parser
     ByteString SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
-> Parser
     ByteString
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser
  ByteString SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
parse_SAM_V1_6_Reference_Sequence_Dictionary_M5)
            Permutation
  (Parser ByteString)
  (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
   -> SAM_V1_6_Reference_Sequence_Dictionary)
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species)
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
      -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
      -> SAM_V1_6_Reference_Sequence_Dictionary)
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_Reference_Sequence_Dictionary_Species
-> Parser
     ByteString (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species)
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
forall a. Maybe a
Nothing
                                         (SAM_V1_6_Reference_Sequence_Dictionary_Species
-> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
forall a. a -> Maybe a
Just (SAM_V1_6_Reference_Sequence_Dictionary_Species
 -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species)
-> Parser ByteString SAM_V1_6_Reference_Sequence_Dictionary_Species
-> Parser
     ByteString (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Reference_Sequence_Dictionary_Species
parse_SAM_V1_6_Reference_Sequence_Dictionary_SP) 
            Permutation
  (Parser ByteString)
  (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
   -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
   -> SAM_V1_6_Reference_Sequence_Dictionary)
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology)
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
      -> SAM_V1_6_Reference_Sequence_Dictionary)
forall a b.
Permutation (Parser ByteString) (a -> b)
-> Permutation (Parser ByteString) a
-> Permutation (Parser ByteString) b
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
-> Parser
     ByteString
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology)
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
forall a. Maybe a
Nothing
                                         (SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
-> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
forall a. a -> Maybe a
Just (SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
 -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology)
-> Parser
     ByteString SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
-> Parser
     ByteString
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser
  ByteString SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
parse_SAM_V1_6_Reference_Sequence_Dictionary_TP)
            Permutation
  (Parser ByteString)
  (Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
   -> SAM_V1_6_Reference_Sequence_Dictionary)
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI)
-> Permutation
     (Parser ByteString) SAM_V1_6_Reference_Sequence_Dictionary
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_Reference_Sequence_Dictionary_URI
-> Parser
     ByteString (Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI)
-> Permutation
     (Parser ByteString)
     (Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
forall a. Maybe a
Nothing
                                         (SAM_V1_6_Reference_Sequence_Dictionary_URI
-> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
forall a. a -> Maybe a
Just (SAM_V1_6_Reference_Sequence_Dictionary_URI
 -> Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI)
-> Parser ByteString SAM_V1_6_Reference_Sequence_Dictionary_URI
-> Parser
     ByteString (Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Reference_Sequence_Dictionary_URI
parse_SAM_V1_6_Reference_Sequence_Dictionary_UR)
  ()
_ <- Parser ByteString ()
endOfLine
  SAM_V1_6_Reference_Sequence_Dictionary
-> Parser SAM_V1_6_Reference_Sequence_Dictionary
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return SAM_V1_6_Reference_Sequence_Dictionary
sq