Safe Haskell | None |
---|---|
Language | Haskell2010 |
Synopsis
- data Fastq = Fastq {}
- streamFastqGzip :: (PrimMonad m, MonadThrow m, MonadResource m) => FilePath -> ConduitT i Fastq m ()
- streamFastq :: (MonadResource m, MonadThrow m) => FilePath -> ConduitT i Fastq m ()
- sinkFastqGzip :: (PrimMonad m, MonadThrow m, MonadResource m) => FilePath -> ConduitT Fastq o m ()
- sinkFastq :: (MonadResource m, MonadThrow m) => FilePath -> ConduitT Fastq o m ()
- parseFastqC :: MonadThrow m => ConduitT ByteString Fastq m ()
- fastqToByteString :: Fastq -> ByteString
- qualitySummary :: Monad m => ConduitT Fastq o m [(Double, Double)]
- trimPolyA :: Int -> Fastq -> Fastq
Documentation
A FASTQ file normally uses four lines per sequence.
- Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line).
- Line 2 is the raw sequence letters.
- Line 3 begins with a
+
character and is optionally followed by the same sequence identifier (and any description) again. - Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.
streamFastqGzip :: (PrimMonad m, MonadThrow m, MonadResource m) => FilePath -> ConduitT i Fastq m () Source #
Read gzipped fastq file.
streamFastq :: (MonadResource m, MonadThrow m) => FilePath -> ConduitT i Fastq m () Source #
sinkFastqGzip :: (PrimMonad m, MonadThrow m, MonadResource m) => FilePath -> ConduitT Fastq o m () Source #
sinkFastq :: (MonadResource m, MonadThrow m) => FilePath -> ConduitT Fastq o m () Source #
parseFastqC :: MonadThrow m => ConduitT ByteString Fastq m () Source #
fastqToByteString :: Fastq -> ByteString Source #