{-# LANGUAGE DeriveDataTypeable #-}
{-# LANGUAGE DeriveGeneric #-}
{-# LANGUAGE FlexibleContexts #-}
{-# LANGUAGE FlexibleInstances #-}
{-# LANGUAGE MultiParamTypeClasses #-}
{-# LANGUAGE OverloadedLists #-}
{-# LANGUAGE OverloadedStrings #-}
{-# LANGUAGE MultiWayIf #-}
{-# LANGUAGE RecordWildCards #-}
{-# LANGUAGE ScopedTypeVariables #-}
{-# LANGUAGE TypeFamilies #-}
{-# Language QuasiQuotes #-}
module Data.SAM.Version1_6.Read.Parser.Alignment.OptionalFields.FOPT (
parse_SAM_V1_6_Alignment_OptionalFields_FOPT
) where
import Data.SAM.Version1_6.Alignment.OptionalFields.FOPT
import Data.SAM.Version1_6.Read.Error
import Data.Attoparsec.ByteString.Char8 as DABC8 (isEndOfLine)
import Data.Attoparsec.ByteString.Lazy as DABL
import qualified Data.ByteString.Char8 as DBC8
import Text.Regex.PCRE.Heavy
parse_SAM_V1_6_Alignment_OptionalFields_FOPT :: Parser SAM_V1_6_Alignment_OptionalFields_FOPT
parse_SAM_V1_6_Alignment_OptionalFields_FOPT :: Parser SAM_V1_6_Alignment_OptionalFields_FOPT
parse_SAM_V1_6_Alignment_OptionalFields_FOPT = do
ByteString
alignmentfoptfieldtag <- do
ByteString
alignmentfoptfieldtagp <-
(Word8 -> Bool) -> Parser ByteString ByteString
DABL.takeTill (Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
58)
case (ByteString
alignmentfoptfieldtagp 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_FOPT_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
alignmentfoptfieldtagp
Word8
_ <-
Word8 -> Parser Word8
word8 Word8
58
()
_ <- do
ByteString
alignmentfoptfieldtypep <-
(Word8 -> Bool) -> Parser ByteString ByteString
DABL.takeTill (Word8 -> Word8 -> Bool
forall a. Eq a => a -> a -> Bool
== Word8
58)
case (ByteString
alignmentfoptfieldtypep ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[f]|]) 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_FOPT_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
Float
alignmentfoptfieldvalue <- do
ByteString
alignmentfoptfieldvaluep <-
(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
alignmentfoptfieldvaluep ByteString -> Regex -> Bool
forall a. ConvertibleStrings a ByteString => a -> Regex -> Bool
=~ [re|[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?|]) of
Bool
False ->
String -> Parser ByteString Float
forall a. String -> Parser ByteString a
forall (m :: * -> *) a. MonadFail m => String -> m a
fail (String -> Parser ByteString Float)
-> String -> Parser ByteString Float
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_FOPT_Value_Incorrect_Format
Bool
True ->
case (ByteString -> Maybe (Integer, ByteString)
DBC8.readInteger ByteString
alignmentfoptfieldvaluep) of
Maybe (Integer, ByteString)
Nothing -> Float -> Parser ByteString Float
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return (-Float
1)
Just (Integer
alignmentfoptfieldvalueinteger,ByteString
_) -> Float -> Parser ByteString Float
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return (Float -> Parser ByteString Float)
-> Float -> Parser ByteString Float
forall a b. (a -> b) -> a -> b
$ (Integer -> Float
forall a. Num a => Integer -> a
fromInteger Integer
alignmentfoptfieldvalueinteger :: Float)
SAM_V1_6_Alignment_OptionalFields_FOPT
-> Parser SAM_V1_6_Alignment_OptionalFields_FOPT
forall a. a -> Parser ByteString a
forall (m :: * -> *) a. Monad m => a -> m a
return SAM_V1_6_Alignment_OptionalFields_FOPT
{ sam_v1_6_alignment_optionalfields_fopt_tag :: ByteString
sam_v1_6_alignment_optionalfields_fopt_tag = ByteString
alignmentfoptfieldtag
, sam_v1_6_alignment_optionalfields_fopt_value :: Float
sam_v1_6_alignment_optionalfields_fopt_value = Float
alignmentfoptfieldvalue
}