{-# 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.HOPT (
parse_SAM_V1_6_Alignment_HOPT
) where
import Data.SAM.Version1_6.Alignment.HOPT
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_HOPT :: Parser SAM_V1_6_Alignment_HOPT
parse_SAM_V1_6_Alignment_HOPT :: Parser SAM_V1_6_Alignment_HOPT
parse_SAM_V1_6_Alignment_HOPT = do
ByteString
alignmenthoptfieldtag <- do ByteString
alignmenthoptfieldtagp <- (Word8 -> Bool) -> Parser ByteString ByteString
DABL.takeTill (Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
58)
case (ByteString
alignmenthoptfieldtagp 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_HOPT_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
alignmenthoptfieldtagp
Word8
_ <- Word8 -> Parser Word8
word8 Word8
58
()
_ <- do ByteString
alignmenthoptfieldtypep <- (Word8 -> Bool) -> Parser ByteString ByteString
DABL.takeTill (Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
58)
case (ByteString
alignmenthoptfieldtypep ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[H]|]) 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_HOPT_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
alignmenthoptfieldvalue <- do ByteString
alignmenthoptfieldvaluep <- (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
alignmenthoptfieldvaluep ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|([0-9A-F][0-9A-F])*|]) 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_HOPT_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
alignmenthoptfieldvaluep
SAM_V1_6_Alignment_HOPT -> Parser SAM_V1_6_Alignment_HOPT
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return SAM_V1_6_Alignment_HOPT { sam_v1_6_alignment_hopt_tag :: ByteString
sam_v1_6_alignment_hopt_tag = ByteString
alignmenthoptfieldtag
, sam_v1_6_alignment_hopt_value :: ByteString
sam_v1_6_alignment_hopt_value = ByteString
alignmenthoptfieldvalue
}