bio-0.5.2: A bioinformatics library

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.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