biopsl-0.2: Library and executables for working with PSL files

Safe HaskellSafe-Infered



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 for details.



data PSL Source

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


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] -> ByteStringSource

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

pslHeader :: ByteStringSource

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