Author Commit Message Labels Comments Date
Brent Pedersen avatarBrent Pedersen
make the interval in an IntervalNode public so it can be traversed.
James Taylor avatarJames Taylor
More documentation on the different between intervalnode and intervaltree.
James Taylor avatarJames Taylor
Another cleanup pass on intersecter interfaces. Simplified interval node, added wrapper class IntervalTree that includes and expands on the old intersecter (that name is still definied for backward compat). Upstream/downstream methods moved out to the wrapper, the nodes only know about left/right queries based on a single position, variants are all in the wrapper.
James Taylor avatarJames Taylor
Make sure pyx doctests are run by setup.py test. Turn off detailed errors (never seems to expand the right part)
James Taylor avatarJames Taylor
IntervalNode can now contain any value, not just Intervals. This eliminates the need for
James Taylor avatarJames Taylor
Adding generated C code for intersection.pyx
James Taylor avatarJames Taylor
Adding an hgignore file
James Taylor avatarJames Taylor
Rebuilding all generated (.pyx) code with Cython 10.3. Fixed a few bugs
James Taylor avatarJames Taylor
Fix issue #2 again.
James Taylor avatarJames Taylor
Backed out changeset a72875307f4b
James Taylor avatarJames Taylor
Fix issue #2 (size problem in interval io).
James Taylor avatarJames Taylor
Patch from Istvan Albert <iua1@psu.edu> to fix some windows compilation
James Taylor avatarJames Taylor
Tests for new Intersecter
James Taylor avatarJames 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 avatarNate Coraor
Require python_lzo in seeklzop.
Guru Ananda avatarGuru Ananda
Small modification to join operation, which should fix the new bug observed today.
Guru Ananda avatarGuru Ananda
Modified intervals join function to include minimum-overlap value.
Bob Harris avatarBob Harris
fixed slicing for -strand reference again; last time I did not get it right; have also added self-test this time
Bob Harris avatarBob Harris
many fixes related to negative strand components
Bob Harris avatarBob Harris
changed error message
Guru Ananda avatarGuru Ananda
Modified BitSetSafeReaderWrapper to use chr, start, end and strand columns from the input dataset, instead of using standard values.
Bob Harris avatarBob Harris
recommitting earlier change, involving correction of how intervals are handled on negative strand
Bob Harris avatarBob Harris
backing out latest change in lieu of testing
Bob Harris avatarBob Harris
fixed problem that occurred when the reference strand was negative
Bob Harris avatarBob Harris
fixed problem that occurred when the reference strand was negative
Daniel Blankenberg avatarDaniel Blankenberg
Add an iterator to AbstractIndexedAccess and AbstractMultiIndexedAccess which returns the index and offset along with the value contained at the offset.
Nate Coraor avatarNate Coraor
Per James, make the build-time numpy dependency conditional (this is so
Daniel Blankenberg avatarDaniel Blankenberg
Remove recursive call from interval.io.BitsetSafeReaderWrapper.next().
James Taylor avatarJames Taylor
Fix for twobit on 64bit platforms (fixes ticket #7)
James Taylor avatarJames Taylor
Make labels optional in newick parser, add tests from markd (fixes ticket #3)
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