{-# 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 #-}
{-# OPTIONS_GHC -fno-warn-name-shadowing #-}
module Data.SAM.Version1_6.Read.Parser.Header.RG.Base (
parse_SAM_V1_6_Read_Group
) where
import Data.SAM.Version1_6.Header
import Data.SAM.Version1_6.Read.Error
import Data.SAM.Version1_6.Read.Parser.Header.RG.ID
import Data.SAM.Version1_6.Read.Parser.Header.RG.BC
import Data.SAM.Version1_6.Read.Parser.Header.RG.CN
import Data.SAM.Version1_6.Read.Parser.Header.RG.DS
import Data.SAM.Version1_6.Read.Parser.Header.RG.DT
import Data.SAM.Version1_6.Read.Parser.Header.RG.FO
import Data.SAM.Version1_6.Read.Parser.Header.RG.KS
import Data.SAM.Version1_6.Read.Parser.Header.RG.LB
import Data.SAM.Version1_6.Read.Parser.Header.RG.PG
import Data.SAM.Version1_6.Read.Parser.Header.RG.PI
import Data.SAM.Version1_6.Read.Parser.Header.RG.PL
import Data.SAM.Version1_6.Read.Parser.Header.RG.PM
import Data.SAM.Version1_6.Read.Parser.Header.RG.PU
import Data.SAM.Version1_6.Read.Parser.Header.RG.SM
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_Read_Group :: Parser SAM_V1_6_Read_Group
parse_SAM_V1_6_Read_Group :: Parser SAM_V1_6_Read_Group
parse_SAM_V1_6_Read_Group = do
()
_ <- do ByteString
rgheaderp <- (Word8 -> Bool) -> Parser ByteString
DABL.takeTill (Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
09)
case (ByteString
rgheaderp ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[@][R][G]|]) 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_Read_Group_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_Read_Group
rg <- Parser Word8
-> Permutation (Parser ByteString) SAM_V1_6_Read_Group
-> Parser SAM_V1_6_Read_Group
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_Read_Group
-> Parser SAM_V1_6_Read_Group)
-> Permutation (Parser ByteString) SAM_V1_6_Read_Group
-> Parser SAM_V1_6_Read_Group
forall a b. (a -> b) -> a -> b
$
SAM_V1_6_Read_Group_Identifier
-> Maybe SAM_V1_6_Read_Group_Barcode_Sequence
-> Maybe SAM_V1_6_Read_Group_Sequencing_Center
-> Maybe SAM_V1_6_Read_Group_Description
-> Maybe SAM_V1_6_Read_Group_Run_Date
-> Maybe SAM_V1_6_Read_Group_Flow_Order
-> Maybe SAM_V1_6_Read_Group_Key_Sequence
-> Maybe SAM_V1_6_Read_Group_Library
-> Maybe SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group
SAM_V1_6_Read_Group
(SAM_V1_6_Read_Group_Identifier
-> Maybe SAM_V1_6_Read_Group_Barcode_Sequence
-> Maybe SAM_V1_6_Read_Group_Sequencing_Center
-> Maybe SAM_V1_6_Read_Group_Description
-> Maybe SAM_V1_6_Read_Group_Run_Date
-> Maybe SAM_V1_6_Read_Group_Flow_Order
-> Maybe SAM_V1_6_Read_Group_Key_Sequence
-> Maybe SAM_V1_6_Read_Group_Library
-> Maybe SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
-> Permutation (Parser ByteString) SAM_V1_6_Read_Group_Identifier
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Barcode_Sequence
-> Maybe SAM_V1_6_Read_Group_Sequencing_Center
-> Maybe SAM_V1_6_Read_Group_Description
-> Maybe SAM_V1_6_Read_Group_Run_Date
-> Maybe SAM_V1_6_Read_Group_Flow_Order
-> Maybe SAM_V1_6_Read_Group_Key_Sequence
-> Maybe SAM_V1_6_Read_Group_Library
-> Maybe SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Read_Group_Identifier
-> Permutation (Parser ByteString) SAM_V1_6_Read_Group_Identifier
forall (m :: * -> *) a. Alternative m => m a -> Permutation m a
toPermutation Parser ByteString SAM_V1_6_Read_Group_Identifier
parse_SAM_V1_6_Read_Group_ID
Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Barcode_Sequence
-> Maybe SAM_V1_6_Read_Group_Sequencing_Center
-> Maybe SAM_V1_6_Read_Group_Description
-> Maybe SAM_V1_6_Read_Group_Run_Date
-> Maybe SAM_V1_6_Read_Group_Flow_Order
-> Maybe SAM_V1_6_Read_Group_Key_Sequence
-> Maybe SAM_V1_6_Read_Group_Library
-> Maybe SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Barcode_Sequence)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Sequencing_Center
-> Maybe SAM_V1_6_Read_Group_Description
-> Maybe SAM_V1_6_Read_Group_Run_Date
-> Maybe SAM_V1_6_Read_Group_Flow_Order
-> Maybe SAM_V1_6_Read_Group_Key_Sequence
-> Maybe SAM_V1_6_Read_Group_Library
-> Maybe SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
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_Barcode_Sequence
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Barcode_Sequence)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Barcode_Sequence)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Read_Group_Barcode_Sequence
forall a. Maybe a
Nothing
(SAM_V1_6_Read_Group_Barcode_Sequence
-> Maybe SAM_V1_6_Read_Group_Barcode_Sequence
forall a. a -> Maybe a
Just (SAM_V1_6_Read_Group_Barcode_Sequence
-> Maybe SAM_V1_6_Read_Group_Barcode_Sequence)
-> Parser ByteString SAM_V1_6_Read_Group_Barcode_Sequence
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Barcode_Sequence)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Read_Group_Barcode_Sequence
parse_SAM_V1_6_Read_Group_BC)
Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Sequencing_Center
-> Maybe SAM_V1_6_Read_Group_Description
-> Maybe SAM_V1_6_Read_Group_Run_Date
-> Maybe SAM_V1_6_Read_Group_Flow_Order
-> Maybe SAM_V1_6_Read_Group_Key_Sequence
-> Maybe SAM_V1_6_Read_Group_Library
-> Maybe SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Sequencing_Center)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Description
-> Maybe SAM_V1_6_Read_Group_Run_Date
-> Maybe SAM_V1_6_Read_Group_Flow_Order
-> Maybe SAM_V1_6_Read_Group_Key_Sequence
-> Maybe SAM_V1_6_Read_Group_Library
-> Maybe SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
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_Sequencing_Center
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Sequencing_Center)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Sequencing_Center)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Read_Group_Sequencing_Center
forall a. Maybe a
Nothing
(SAM_V1_6_Read_Group_Sequencing_Center
-> Maybe SAM_V1_6_Read_Group_Sequencing_Center
forall a. a -> Maybe a
Just (SAM_V1_6_Read_Group_Sequencing_Center
-> Maybe SAM_V1_6_Read_Group_Sequencing_Center)
-> Parser ByteString SAM_V1_6_Read_Group_Sequencing_Center
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Sequencing_Center)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Read_Group_Sequencing_Center
parse_SAM_V1_6_Read_Group_CN)
Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Description
-> Maybe SAM_V1_6_Read_Group_Run_Date
-> Maybe SAM_V1_6_Read_Group_Flow_Order
-> Maybe SAM_V1_6_Read_Group_Key_Sequence
-> Maybe SAM_V1_6_Read_Group_Library
-> Maybe SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Description)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Run_Date
-> Maybe SAM_V1_6_Read_Group_Flow_Order
-> Maybe SAM_V1_6_Read_Group_Key_Sequence
-> Maybe SAM_V1_6_Read_Group_Library
-> Maybe SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
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_Description
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Description)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Description)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Read_Group_Description
forall a. Maybe a
Nothing
(SAM_V1_6_Read_Group_Description
-> Maybe SAM_V1_6_Read_Group_Description
forall a. a -> Maybe a
Just (SAM_V1_6_Read_Group_Description
-> Maybe SAM_V1_6_Read_Group_Description)
-> Parser ByteString SAM_V1_6_Read_Group_Description
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Description)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Read_Group_Description
parse_SAM_V1_6_Read_Group_DS)
Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Run_Date
-> Maybe SAM_V1_6_Read_Group_Flow_Order
-> Maybe SAM_V1_6_Read_Group_Key_Sequence
-> Maybe SAM_V1_6_Read_Group_Library
-> Maybe SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Run_Date)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Flow_Order
-> Maybe SAM_V1_6_Read_Group_Key_Sequence
-> Maybe SAM_V1_6_Read_Group_Library
-> Maybe SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
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_Run_Date
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Run_Date)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Run_Date)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Read_Group_Run_Date
forall a. Maybe a
Nothing
(SAM_V1_6_Read_Group_Run_Date -> Maybe SAM_V1_6_Read_Group_Run_Date
forall a. a -> Maybe a
Just (SAM_V1_6_Read_Group_Run_Date
-> Maybe SAM_V1_6_Read_Group_Run_Date)
-> Parser ByteString SAM_V1_6_Read_Group_Run_Date
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Run_Date)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Read_Group_Run_Date
parse_SAM_V1_6_Read_Group_DT)
Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Flow_Order
-> Maybe SAM_V1_6_Read_Group_Key_Sequence
-> Maybe SAM_V1_6_Read_Group_Library
-> Maybe SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Flow_Order)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Key_Sequence
-> Maybe SAM_V1_6_Read_Group_Library
-> Maybe SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
forall a b.
Permutation (Parser ByteString) (a -> b)
-> Permutation (Parser ByteString) a
-> Permutation (Parser ByteString) b
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Maybe SAM_V1_6_Read_Group_Flow_Order
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Flow_Order)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Flow_Order)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Read_Group_Flow_Order
forall a. Maybe a
Nothing
(SAM_V1_6_Read_Group_Flow_Order
-> Maybe SAM_V1_6_Read_Group_Flow_Order
forall a. a -> Maybe a
Just (SAM_V1_6_Read_Group_Flow_Order
-> Maybe SAM_V1_6_Read_Group_Flow_Order)
-> Parser ByteString SAM_V1_6_Read_Group_Flow_Order
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Flow_Order)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Read_Group_Flow_Order
parse_SAM_V1_6_Read_Group_FO)
Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Key_Sequence
-> Maybe SAM_V1_6_Read_Group_Library
-> Maybe SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Key_Sequence)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Library
-> Maybe SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
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_Key_Sequence
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Key_Sequence)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Key_Sequence)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Read_Group_Key_Sequence
forall a. Maybe a
Nothing
(SAM_V1_6_Read_Group_Key_Sequence
-> Maybe SAM_V1_6_Read_Group_Key_Sequence
forall a. a -> Maybe a
Just (SAM_V1_6_Read_Group_Key_Sequence
-> Maybe SAM_V1_6_Read_Group_Key_Sequence)
-> Parser ByteString SAM_V1_6_Read_Group_Key_Sequence
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Key_Sequence)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Read_Group_Key_Sequence
parse_SAM_V1_6_Read_Group_KS)
Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Library
-> Maybe SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Library)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
forall a b.
Permutation (Parser ByteString) (a -> b)
-> Permutation (Parser ByteString) a
-> Permutation (Parser ByteString) b
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Maybe SAM_V1_6_Read_Group_Library
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Library)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Library)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Read_Group_Library
forall a. Maybe a
Nothing
(SAM_V1_6_Read_Group_Library -> Maybe SAM_V1_6_Read_Group_Library
forall a. a -> Maybe a
Just (SAM_V1_6_Read_Group_Library -> Maybe SAM_V1_6_Read_Group_Library)
-> Parser ByteString SAM_V1_6_Read_Group_Library
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Library)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Read_Group_Library
parse_SAM_V1_6_Read_Group_LB)
Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Programs)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
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_Programs
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Programs)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Programs)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Read_Group_Programs
forall a. Maybe a
Nothing
(SAM_V1_6_Read_Group_Programs -> Maybe SAM_V1_6_Read_Group_Programs
forall a. a -> Maybe a
Just (SAM_V1_6_Read_Group_Programs
-> Maybe SAM_V1_6_Read_Group_Programs)
-> Parser ByteString SAM_V1_6_Read_Group_Programs
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Programs)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Read_Group_Programs
parse_SAM_V1_6_Read_Group_PG)
Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
forall a b.
Permutation (Parser ByteString) (a -> b)
-> Permutation (Parser ByteString) a
-> Permutation (Parser ByteString) b
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Parser
ByteString (Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
forall a. Maybe a
Nothing
(SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
forall a. a -> Maybe a
Just (SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size)
-> Parser
ByteString SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
-> Parser
ByteString (Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
parse_SAM_V1_6_Read_Group_PI)
Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Platform)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
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_Platform
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Platform)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Platform)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Read_Group_Platform
forall a. Maybe a
Nothing
(SAM_V1_6_Read_Group_Platform -> Maybe SAM_V1_6_Read_Group_Platform
forall a. a -> Maybe a
Just (SAM_V1_6_Read_Group_Platform
-> Maybe SAM_V1_6_Read_Group_Platform)
-> Parser ByteString SAM_V1_6_Read_Group_Platform
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Platform)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Read_Group_Platform
parse_SAM_V1_6_Read_Group_PL)
Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample
-> SAM_V1_6_Read_Group)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Platform_Model)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample -> SAM_V1_6_Read_Group)
forall a b.
Permutation (Parser ByteString) (a -> b)
-> Permutation (Parser ByteString) a
-> Permutation (Parser ByteString) b
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Maybe SAM_V1_6_Read_Group_Platform_Model
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Platform_Model)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Platform_Model)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Read_Group_Platform_Model
forall a. Maybe a
Nothing
(SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Model
forall a. a -> Maybe a
Just (SAM_V1_6_Read_Group_Platform_Model
-> Maybe SAM_V1_6_Read_Group_Platform_Model)
-> Parser ByteString SAM_V1_6_Read_Group_Platform_Model
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Platform_Model)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Read_Group_Platform_Model
parse_SAM_V1_6_Read_Group_PM)
Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Sample -> SAM_V1_6_Read_Group)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Platform_Unit)
-> Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Sample -> SAM_V1_6_Read_Group)
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_Platform_Unit
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Platform_Unit)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Platform_Unit)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Read_Group_Platform_Unit
forall a. Maybe a
Nothing
(SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Platform_Unit
forall a. a -> Maybe a
Just (SAM_V1_6_Read_Group_Platform_Unit
-> Maybe SAM_V1_6_Read_Group_Platform_Unit)
-> Parser ByteString SAM_V1_6_Read_Group_Platform_Unit
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Platform_Unit)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Read_Group_Platform_Unit
parse_SAM_V1_6_Read_Group_PU)
Permutation
(Parser ByteString)
(Maybe SAM_V1_6_Read_Group_Sample -> SAM_V1_6_Read_Group)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Sample)
-> Permutation (Parser ByteString) SAM_V1_6_Read_Group
forall a b.
Permutation (Parser ByteString) (a -> b)
-> Permutation (Parser ByteString) a
-> Permutation (Parser ByteString) b
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Maybe SAM_V1_6_Read_Group_Sample
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Sample)
-> Permutation
(Parser ByteString) (Maybe SAM_V1_6_Read_Group_Sample)
forall (m :: * -> *) a.
Alternative m =>
a -> m a -> Permutation m a
toPermutationWithDefault Maybe SAM_V1_6_Read_Group_Sample
forall a. Maybe a
Nothing
(SAM_V1_6_Read_Group_Sample -> Maybe SAM_V1_6_Read_Group_Sample
forall a. a -> Maybe a
Just (SAM_V1_6_Read_Group_Sample -> Maybe SAM_V1_6_Read_Group_Sample)
-> Parser ByteString SAM_V1_6_Read_Group_Sample
-> Parser ByteString (Maybe SAM_V1_6_Read_Group_Sample)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser ByteString SAM_V1_6_Read_Group_Sample
parse_SAM_V1_6_Read_Group_SM)
()
_ <- Parser ByteString ()
endOfLine
SAM_V1_6_Read_Group -> Parser SAM_V1_6_Read_Group
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return SAM_V1_6_Read_Group
rg