{-# 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.Alignment.AOPT (
parse_SAM_V1_6_Alignment_AOPT
) where
import Data.SAM.Version1_6.Alignment.AOPT
import Data.SAM.Version1_6.Read.Error
import Data.Attoparsec.ByteString.Char8 as DABC8 (isEndOfLine)
import Data.Attoparsec.ByteString.Lazy as DABL
import Text.Regex.PCRE.Heavy
parse_SAM_V1_6_Alignment_AOPT :: Parser SAM_V1_6_Alignment_AOPT
parse_SAM_V1_6_Alignment_AOPT :: Parser SAM_V1_6_Alignment_AOPT
parse_SAM_V1_6_Alignment_AOPT = do
ByteString
alignmentaoptfieldtag <- do ByteString
alignmentaoptfieldtagp <- (Word8 -> Bool) -> Parser ByteString ByteString
DABL.takeTill (Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
58)
case (ByteString
alignmentaoptfieldtagp ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[A-Za-z][A-Za-z0-9]|]) of
Bool
False -> String -> Parser ByteString ByteString
forall a. String -> Parser ByteString a
forall (m :: * -> *) a. MonadFail m => String -> m a
fail (String -> Parser ByteString ByteString)
-> String -> Parser ByteString 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_Alignment_AOPT_Tag_Incorrect_Format
Bool
True ->
ByteString -> Parser ByteString ByteString
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return ByteString
alignmentaoptfieldtagp
Word8
_ <- Word8 -> Parser Word8
word8 Word8
58
()
_ <- do ByteString
alignmentaoptfieldtypep <- (Word8 -> Bool) -> Parser ByteString ByteString
DABL.takeTill (Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
58)
case (ByteString
alignmentaoptfieldtypep ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[A]|]) 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_Alignment_AOPT_Type_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
58
ByteString
alignmentaoptfieldvalue <- do ByteString
alignmentaoptfieldvaluep <- (Word8 -> Bool) -> Parser ByteString ByteString
DABL.takeTill (\Word8
x -> Word8
x Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
09 Bool -> Bool -> Bool
|| Word8 -> Bool
isEndOfLine Word8
x)
case (ByteString
alignmentaoptfieldvaluep ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[!-~]|]) of
Bool
False -> String -> Parser ByteString ByteString
forall a. String -> Parser ByteString a
forall (m :: * -> *) a. MonadFail m => String -> m a
fail (String -> Parser ByteString ByteString)
-> String -> Parser ByteString 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_Alignment_AOPT_Value_Incorrect_Format
Bool
True ->
ByteString -> Parser ByteString ByteString
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return ByteString
alignmentaoptfieldvaluep
SAM_V1_6_Alignment_AOPT -> Parser SAM_V1_6_Alignment_AOPT
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return SAM_V1_6_Alignment_AOPT { sam_v1_6_alignment_aopt_tag :: ByteString
sam_v1_6_alignment_aopt_tag = ByteString
alignmentaoptfieldtag
, sam_v1_6_alignment_aopt_value :: ByteString
sam_v1_6_alignment_aopt_value = ByteString
alignmentaoptfieldvalue
}