Bio.Data.Fastq

Documentation

data Fastq

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.

Constructors

Fastq

Fields

• fastqSeqId :: ByteString
• fastqSeq :: ByteString
• fastqSeqQual :: ByteString

Instances

Eq Fastq

Defined in Bio.Data.Fastq

Methods

(==) :: Fastq -> Fastq -> Bool

(/=) :: Fastq -> Fastq -> Bool

Show Fastq

Defined in Bio.Data.Fastq

Methods

showsPrec :: Int -> Fastq -> ShowS

show :: Fastq -> String

showList :: [Fastq] -> ShowS

Generic Fastq

Defined in Bio.Data.Fastq

Associated Types

type Rep Fastq :: Type -> Type

Methods

from :: Fastq -> Rep Fastq x

to :: Rep Fastq x -> Fastq

NFData Fastq

Defined in Bio.Data.Fastq

Methods

rnf :: Fastq -> ()

type Rep Fastq

Defined in Bio.Data.Fastq

type Rep Fastq = D1 ('MetaData "Fastq" "Bio.Data.Fastq" "bioinformatics-toolkit-0.10.0-A8Y5r7ZpZ9gGDfktm9e6ZK" 'False) (C1 ('MetaCons "Fastq" 'PrefixI 'True) (S1 ('MetaSel ('Just "fastqSeqId") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString) :*: (S1 ('MetaSel ('Just "fastqSeq") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString) :*: S1 ('MetaSel ('Just "fastqSeqQual") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))))

streamFastqGzip :: (PrimMonad m, MonadThrow m, MonadResource m) => FilePath -> ConduitT i Fastq m ()

Read gzipped fastq file.

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 :: Monad m => ConduitT ByteString Fastq m ()

parseFastqC' :: MonadThrow m => ConduitT ByteString Fastq m ()

fastqToByteString :: Fastq -> ByteString

qualitySummary :: Monad m => ConduitT Fastq o m [(Double, Double)]

Get the mean and variance of quality scores at every position.

trimPolyA :: Int -> Fastq -> Fastq

Remove trailing A