{-# 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 (
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
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)
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 ->
() -> Parser ByteString ()
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return ()
Word8
_ <- Word8 -> Parser Word8
word8 Word8
09
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