{-# 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.HD.Base (
parse_SAM_V1_6_File_Level_Metadata
) where
import Data.SAM.Version1_6.Header
import Data.SAM.Version1_6.Read.Error
import Data.SAM.Version1_6.Read.Parser.Header.HD.VN
import Data.SAM.Version1_6.Read.Parser.Header.HD.SO
import Data.SAM.Version1_6.Read.Parser.Header.HD.GO
import Data.SAM.Version1_6.Read.Parser.Header.HD.SS
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_File_Level_Metadata :: Parser SAM_V1_6_File_Level_Metadata
parse_SAM_V1_6_File_Level_Metadata :: Parser SAM_V1_6_File_Level_Metadata
parse_SAM_V1_6_File_Level_Metadata = do
()
_ <- do ByteString
hdheaderp <- (Word8 -> Bool) -> Parser ByteString
DABL.takeTill (Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
09)
case (ByteString
hdheaderp ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[@][H][D]|]) 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_File_Level_Metadata
hd <- Parser Word8
-> Permutation (Parser ByteString) SAM_V1_6_File_Level_Metadata
-> Parser SAM_V1_6_File_Level_Metadata
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_File_Level_Metadata
-> Parser SAM_V1_6_File_Level_Metadata)
-> Permutation (Parser ByteString) SAM_V1_6_File_Level_Metadata
-> Parser SAM_V1_6_File_Level_Metadata
forall a b. (a -> b) -> a -> b
$
SAM_V1_6_File_Level_Metadata_Format_Version
-> Maybe SAM_V1_6_File_Level_Metadata_Sorting_Order
-> Maybe SAM_V1_6_File_Level_Metadata_Alignment_Grouping
-> Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order
-> SAM_V1_6_File_Level_Metadata
SAM_V1_6_File_Level_Metadata
(SAM_V1_6_File_Level_Metadata_Format_Version
-> Maybe SAM_V1_6_File_Level_Metadata_Sorting_Order
-> Maybe SAM_V1_6_File_Level_Metadata_Alignment_Grouping
-> Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order
-> SAM_V1_6_File_Level_Metadata)
-> Permutation
(Parser ByteString) SAM_V1_6_File_Level_Metadata_Format_Version
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_File_Level_Metadata_Sorting_Order
-> Maybe SAM_V1_6_File_Level_Metadata_Alignment_Grouping
-> Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order
-> SAM_V1_6_File_Level_Metadata)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_File_Level_Metadata_Format_Version
-> Permutation
(Parser ByteString) SAM_V1_6_File_Level_Metadata_Format_Version
forall (m :: * -> *) a. Alternative m => m a -> Permutation m a
toPermutation Parser ByteString SAM_V1_6_File_Level_Metadata_Format_Version
parse_SAM_V1_6_File_Level_Metadata_VN
Permutation
(Parser ByteString)
(Maybe SAM_V1_6_File_Level_Metadata_Sorting_Order
-> Maybe SAM_V1_6_File_Level_Metadata_Alignment_Grouping
-> Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order
-> SAM_V1_6_File_Level_Metadata)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_File_Level_Metadata_Sorting_Order)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_File_Level_Metadata_Alignment_Grouping
-> Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order
-> SAM_V1_6_File_Level_Metadata)
forall a b.
Permutation (Parser ByteString) (a -> b)
-> Permutation (Parser ByteString) a
-> Permutation (Parser ByteString) b
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Maybe SAM_V1_6_File_Level_Metadata_Sorting_Order
-> Parser
ByteString (Maybe SAM_V1_6_File_Level_Metadata_Sorting_Order)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_File_Level_Metadata_Sorting_Order)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_File_Level_Metadata_Sorting_Order
forall a. Maybe a
Nothing
(SAM_V1_6_File_Level_Metadata_Sorting_Order
-> Maybe SAM_V1_6_File_Level_Metadata_Sorting_Order
forall a. a -> Maybe a
Just (SAM_V1_6_File_Level_Metadata_Sorting_Order
-> Maybe SAM_V1_6_File_Level_Metadata_Sorting_Order)
-> Parser ByteString SAM_V1_6_File_Level_Metadata_Sorting_Order
-> Parser
ByteString (Maybe SAM_V1_6_File_Level_Metadata_Sorting_Order)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_File_Level_Metadata_Sorting_Order
parse_SAM_V1_6_File_Level_Metadata_SO)
Permutation
(Parser ByteString)
(Maybe SAM_V1_6_File_Level_Metadata_Alignment_Grouping
-> Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order
-> SAM_V1_6_File_Level_Metadata)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_File_Level_Metadata_Alignment_Grouping)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order
-> SAM_V1_6_File_Level_Metadata)
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_File_Level_Metadata_Alignment_Grouping
-> Parser
ByteString (Maybe SAM_V1_6_File_Level_Metadata_Alignment_Grouping)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_File_Level_Metadata_Alignment_Grouping)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_File_Level_Metadata_Alignment_Grouping
forall a. Maybe a
Nothing
(SAM_V1_6_File_Level_Metadata_Alignment_Grouping
-> Maybe SAM_V1_6_File_Level_Metadata_Alignment_Grouping
forall a. a -> Maybe a
Just (SAM_V1_6_File_Level_Metadata_Alignment_Grouping
-> Maybe SAM_V1_6_File_Level_Metadata_Alignment_Grouping)
-> Parser
ByteString SAM_V1_6_File_Level_Metadata_Alignment_Grouping
-> Parser
ByteString (Maybe SAM_V1_6_File_Level_Metadata_Alignment_Grouping)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_File_Level_Metadata_Alignment_Grouping
parse_SAM_V1_6_File_Level_Metadata_GO)
Permutation
(Parser ByteString)
(Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order
-> SAM_V1_6_File_Level_Metadata)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order)
-> Permutation (Parser ByteString) SAM_V1_6_File_Level_Metadata
forall a b.
Permutation (Parser ByteString) (a -> b)
-> Permutation (Parser ByteString) a
-> Permutation (Parser ByteString) b
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order
-> Parser
ByteString (Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order
forall a. Maybe a
Nothing
(SAM_V1_6_File_Level_Metadata_SubSorting_Order
-> Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order
forall a. a -> Maybe a
Just (SAM_V1_6_File_Level_Metadata_SubSorting_Order
-> Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order)
-> Parser ByteString SAM_V1_6_File_Level_Metadata_SubSorting_Order
-> Parser
ByteString (Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_File_Level_Metadata_SubSorting_Order
parse_SAM_V1_6_File_Level_Metadata_SS)
()
_ <- Parser ByteString ()
endOfLine
SAM_V1_6_File_Level_Metadata -> Parser SAM_V1_6_File_Level_Metadata
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return SAM_V1_6_File_Level_Metadata
hd