Safe Haskell	Safe-Infered

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 Source

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

Constructors

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

Instances

Eq PSL
Show PSL

readPSL :: FilePath -> IO [PSL]Source

Read and parse a PSL file.

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

Create a PSL file from a list of alignments.

parsePSL :: ByteString -> [PSL]Source

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

unparsePSL :: [PSL] -> ByteString Source

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

pslHeader :: ByteString Source

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