Safe Haskell	None
Language	Haskell2010

Bio.Parse.Sequence.FastQ

Synopsis

Documentation

data FastQSequence #

Constructors

FastQSequence
Fields _header :: [ByteString] _sequence :: ByteString _quality :: ByteString

Instances

Eq FastQSequence #
Methods (==) :: FastQSequence -> FastQSequence -> Bool # (/=) :: FastQSequence -> FastQSequence -> Bool #
Ord FastQSequence #
Methods compare :: FastQSequence -> FastQSequence -> Ordering # (<) :: FastQSequence -> FastQSequence -> Bool # (<=) :: FastQSequence -> FastQSequence -> Bool # (>) :: FastQSequence -> FastQSequence -> Bool # (>=) :: FastQSequence -> FastQSequence -> Bool # max :: FastQSequence -> FastQSequence -> FastQSequence # min :: FastQSequence -> FastQSequence -> FastQSequence #
Show FastQSequence #
Methods showsPrec :: Int -> FastQSequence -> ShowS # show :: FastQSequence -> String # showList :: [FastQSequence] -> ShowS #
SequenceParser FastQSequence #
Methods parseSequence :: ParseConstraint m => m FastQSequence # parseSequences :: ParseConstraint m => m [FastQSequence] #

sequence :: Lens' FastQSequence ByteString #

quality :: Lens' FastQSequence ByteString #

header :: Lens' FastQSequence [ByteString] #

parseHeader :: ParseConstraint m => m [ByteString] #

Parses the header of a FASTQ file.

The header starts with a @ character and follows with an optional description. When making use if BioSeq, the first word of the header is used as the seqid.

parseSequenceLine :: ParseConstraint m => m ByteString #

Parses the line of sequence data.

parseQualityLine :: ParseConstraint m => m ByteString #

Parses the line of quality data.

parseSequence' :: ParseConstraint m => m FastQSequence #

Parses an entire sequence including its header and quality data.

parseSequences' :: ParseConstraint m => m [FastQSequence] #

Parses many sequences.