| bio-0.4.6: A bioinformatics library | Source code | Contents | Index

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 | Source

Constructors

PSL |

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

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

parsePSL :: ByteString -> [PSL] | Source

unparsePSL :: [PSL] -> ByteString | Source

pslHeader :: ByteString | Source

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