Safe Haskell	None
Language	Haskell2010

SequenceFormats.Pileup

Synopsis

readPileupFromStdIn :: (MonadIO m, MonadThrow m) => Producer PileupRow m ()
readPileupFromFile :: MonadSafe m => FilePath -> Producer PileupRow m ()
data PileupRow = PileupRow {
- pileupChrom :: Chrom
- pileupPos :: Int
- pileupRef :: Char
- pileupBases :: [String]
- pileupStrandInfo :: [[Strand]]
}
data Strand
- = ForwardStrand
- | ReverseStrand

Documentation

readPileupFromStdIn :: (MonadIO m, MonadThrow m) => Producer PileupRow m () Source #

Read a pileup-formatted file from StdIn, for reading from an external command `samtools mpileup`.

readPileupFromFile :: MonadSafe m => FilePath -> Producer PileupRow m () Source #

Read pileup from a file.

data PileupRow Source #

A datatype to represent a single pileup row for multiple individuals. The constructor arguments are: Chromosome, Position, Refererence Allelele, Pileup String per individual

Constructors

PileupRow
Fields pileupChrom :: Chrom The chromosome pileupPos :: Int The position pileupRef :: Char The reference base pileupBases :: [String] The base string pileupStrandInfo :: [[Strand]]

Instances

Eq PileupRow Source #
Instance details Defined in SequenceFormats.Pileup Methods (==) :: PileupRow -> PileupRow -> Bool # (/=) :: PileupRow -> PileupRow -> Bool #
Show PileupRow Source #
Instance details Defined in SequenceFormats.Pileup Methods showsPrec :: Int -> PileupRow -> ShowS # show :: PileupRow -> String # showList :: [PileupRow] -> ShowS #

data Strand Source #

A datatype to represent the strand orientation of a single base.

Constructors

ForwardStrand
ReverseStrand

Instances

Eq Strand Source #
Instance details Defined in SequenceFormats.Pileup Methods (==) :: Strand -> Strand -> Bool # (/=) :: Strand -> Strand -> Bool #
Show Strand Source #
Instance details Defined in SequenceFormats.Pileup Methods showsPrec :: Int -> Strand -> ShowS # show :: Strand -> String # showList :: [Strand] -> ShowS #