Commits

Author Commit Message Labels Comments Date
James Taylor
Fix issue #2 again.
James Taylor
Backed out changeset a72875307f4b Accidently included generated code.
James Taylor
Fix issue #2 (size problem in interval io).
James Taylor
Patch from Istvan Albert <iua1@psu.edu> to fix some windows compilation issues in bitsets and to disable some modules that currently don't compile in windows.
James Taylor
Tests for new Intersecter
James Taylor
Integrate Cython version of quicksect from Brent Pederson. This replaces the old intersection package with a much faster and more functional version. API compatibility should be maintained
Nate Coraor
Require python_lzo in seeklzop.
Guru Ananda
Small modification to join operation, which should fix the new bug observed today.
Guru Ananda
Modified intervals join function to include minimum-overlap value.
Bob Harris
fixed slicing for -strand reference again; last time I did not get it right; have also added self-test this time
Bob Harris
many fixes related to negative strand components
Bob Harris
changed error message
Guru Ananda
Modified BitSetSafeReaderWrapper to use chr, start, end and strand columns from the input dataset, instead of using standard values.
Bob Harris
recommitting earlier change, involving correction of how intervals are handled on negative strand
Bob Harris
backing out latest change in lieu of testing
Bob Harris
fixed problem that occurred when the reference strand was negative
Bob Harris
fixed problem that occurred when the reference strand was negative
Daniel Blankenberg
Add an iterator to AbstractIndexedAccess and AbstractMultiIndexedAccess which returns the index and offset along with the value contained at the offset.
Nate Coraor
Per James, make the build-time numpy dependency conditional (this is so people building for their own platforms need not have numpy).
Daniel Blankenberg
Remove recursive call from interval.io.BitsetSafeReaderWrapper.next().
James Taylor
Fix for twobit on 64bit platforms (fixes ticket #7)
James Taylor
Make labels optional in newick parser, add tests from markd (fixes ticket #3)
James Taylor
Update pyparsing to latest version (1.5.0)
James Taylor
Fix comparisons operations (from markd@soe.ucsc.edu, fixes ticket #4)
James Taylor
Do not pkg_resource.require bx-python from inside bx-python
James Taylor
Include TY (type) lines in motif parsing
James Taylor
Fix package data (for template.ps)
James Taylor
Support for optional short options (specifying a long option only) in doc_optparse.
James Taylor
Writer for transfac format, parser now handles "BS" lines as produced by CREAD.
James Taylor
Use sorted alphabet for drawing logos.
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