Commits

Author Commit Message Labels Comments Date
Ian Schenk
Changed join to be more reliable and not require sorted input.
Ian Schenk
coverage was inappropriately mangling output by omitting intervals on chromosomes not in the secondary qeries.
Ian Schenk
bug fix in concat
Bob Harris
added support for codebook, as separate file or embedded in the quantum sequence file
James Taylor
coverage by interval
James Taylor
Fixes. Aggregate now takes a mask.
Bob Harris
added support for quantum sequences; minor cleanup; added test suite
Ian Schenk
Moved the join operation into here (bx) instead of being solely in galaxy. It requires inputs to be sorted by chrom(lexicographically) start(arithmetically) and end(arithmetically) to function properly.
Ian Schenk
Updated find clusters to use smarter distance, which allows 0 or negatives to indicate touching or overlapping respectively (as per requested).
Ian Schenk
Tweaked find_clusters to return comments as well.
Ian Schenk
Added complement operation. A bit naive at the moment since the chromInfo is assumed to be in memory, and some chromInfo tables of incomplete databases are quite large (5 MB) due to scaffolds.
Bob Harris
restoring stdout from __stdout; added stdout intercept to a few more modules; fasta tests had been left out of the overall test set
Bob Harris
tests will now fail if someone leaves debug prints lying around ;)
Ian Schenk
Fixed for incorrectly referenced columns in coverage
James Taylor
Yay, debug statements that corrupt my output!
Bob Harris
minor improvement the species_to_lengths mechanism
Bob Harris
I don't understand why previous statement was legal python
Bob Harris
improved reporting of unrecognized sequence file formats
James Taylor
More mapping tests, fixes in intersect for the boolean output case, maf_tile_2 can now work on mafs without synteny information (though not
Ian Schenk
Yet another bug fix for subtract.
Ian Schenk
Similar bug fix for subtract. Headerless files were breaking.
Ian Schenk
Bug fix in intersect.
Bob Harris
was out-of-date with latest alignment class; added a few prettifying options
Ian Schenk
Fixed random numbers, using binomial distribution now.
Bob Harris
Bob Harris
(missed commit for this on Apr/7/2006), species_to_length now is more forgiving of certain alignment src names
Bob Harris
sequence readers are now supported (i.e. iterate over sequences in a fasta file)
Ian Schenk
Added find_clusters.
Bob Harris
script to convert lav file to maf, name changes in maf_to_axt
Ian Schenk
Fixed merge to maintain proper columns throughout file
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