Safe Haskell	Safe
Language	Haskell98

Bio.Alignment.PSL

Description

This models the PSL format used by e.g. the alignment tool BLAT. It is a simple, textual representation of (spliced) alignments, with tab-separated fields.

See http://genome.ucsc.edu/FAQ/FAQformat#format2 for details.

Synopsis

Documentation

data PSL #

This encodes a PSL record, corresponding to one line of the PSL file.

Constructors

PSL
Fields match, mismatch, repmatch, ncount, qgapcount, qgaplength, tgapcount, tgaplength :: Int strand :: ByteString qname :: ByteString qsize, qstart, qend :: Int tname :: ByteString tsize, tstart, tend :: Int blockcount :: Int blocksizes, qstarts, tstarts :: [Int]

Instances

Eq PSL #
Methods (==) :: PSL -> PSL -> Bool # (/=) :: PSL -> PSL -> Bool #
Show PSL #
Methods showsPrec :: Int -> PSL -> ShowS # show :: PSL -> String # showList :: [PSL] -> ShowS #

readPSL :: FilePath -> IO [PSL] #

Read and parse a PSL file.

writePSL :: FilePath -> [PSL] -> IO () #

Create a PSL file from a list of alignments.

printPSL :: [PSL] -> IO () #

parsePSL :: ByteString -> [PSL] #

Parse a ByteString as a PSL file (note that it must contain the PSL header).

unparsePSL :: [PSL] -> ByteString #

Unparse a list of PSL alignments encoding them into a ByteString (not including PSL header).

pslHeader :: ByteString #

The PSL header (version 3), as a ByteString.