{-# 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
-- 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.RG.Base ( -- * SAM_V1_6 parser - header section (Read group)
                                                        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

-- | @"SAM_V1_6_Read_Group"@ parser.
--
-- Defines a parser for @RG 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_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)
                  -- Parse @RG tag of the header section.
                  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  -> -- @RG 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
  -- ID, BC, CN, DS, DT, FO, KS, LB, PG, PI, PL,
  -- PM, PU and SM tags can appear in any order.
  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