hs-samtools-0.5.0.2: src/Data/SAM/Version1_6/Read/Parser/Header/RG/Base.hs
{-# LANGUAGE DeriveDataTypeable #-}
{-# LANGUAGE DeriveGeneric #-}
{-# LANGUAGE FlexibleContexts #-}
{-# LANGUAGE FlexibleInstances #-}
{-# LANGUAGE MultiParamTypeClasses #-}
{-# LANGUAGE OverloadedLists #-}
{-# LANGUAGE OverloadedStrings #-}
{-# LANGUAGE MultiWayIf #-}
{-# LANGUAGE PackageImports #-}
{-# LANGUAGE RecordWildCards #-}
{-# LANGUAGE ScopedTypeVariables #-}
{-# LANGUAGE TemplateHaskell #-}
{-# 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 Data.Attoparsec.ByteString.Lazy as DABL
import Text.Regex.PCRE.Heavy
-- | Make a parser optional, return Nothing if there is no match.
maybeOption :: Parser a
-> Parser (Maybe a)
maybeOption p = option Nothing (Just <$> p)
-- | @"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 = do
_ <- do rgheaderp <- DABL.takeTill (== 09)
-- Parse @RG tag of the header section.
case (rgheaderp =~ [re|[@][R][G]|]) of
False -> fail $ show SAM_V1_6_Error_Read_Group_Tag_Incorrect_Format
True -> -- @RG tag is in the accepted format.
return rgheaderp
_ <- word8 09
-- This parser assumes that the ID tag always appears first, followed by
-- the BC, CN, DS, DT, FO, KS, LB, PG, PI, PL,
-- PM, PU and SM tags if they exist, in that order.
id <- parse_SAM_V1_6_SAM_V1_6_Read_Group_ID
_ <- word8 09
bc <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_BC
_ <- word8 09
cn <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_CN
_ <- word8 09
ds <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_DS
_ <- word8 09
dt <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_DT
_ <- word8 09
fo <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_FO
_ <- word8 09
ks <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_KS
_ <- word8 09
lb <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_LB
_ <- word8 09
pg <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_PG
_ <- word8 09
pi <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_PI
_ <- word8 09
pl <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_PL
_ <- word8 09
pm <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_PM
_ <- word8 09
pu <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_PU
_ <- word8 09
sm <- maybeOption parse_SAM_V1_6_SAM_V1_6_Read_Group_SM
return SAM_V1_6_Read_Group { sam_v1_6_read_group_identifer = id
, sam_v1_6_read_group_barcode_sequence = bc
, sam_v1_6_read_group_sequencing_center = cn
, sam_v1_6_read_group_description = ds
, sam_v1_6_read_group_run_date = dt
, sam_v1_6_read_group_flow_order = fo
, sam_v1_6_read_group_key_sequence = ks
, sam_v1_6_read_group_library = lb
, sam_v1_6_read_group_programs = pg
, sam_v1_6_read_group_predicted_median_insert_size = pi
, sam_v1_6_read_group_platform = pl
, sam_v1_6_read_group_platform_model = pm
, sam_v1_6_read_group_platform_unit = pu
, sam_v1_6_read_group_sample = sm
}