Bio.Alignment.PSL

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.eduFAQFAQformat#format2 for details.

Documentation

data PSL

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]

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

parsePSL :: ByteString -> [PSL]

unparsePSL :: [PSL] -> ByteString

pslHeader :: ByteString