Commits

Author Commit Message Labels Comments Date
James Taylor
Moving maf_covered_ranges.py util from ESPERR
James Taylor
Don't fail on missing lzo unless actually used
James Taylor
Run everything through Cython 0.18. Fixed a bug in BinnedBitset when the size is larger than the max size, all tests passing
James Taylor
Updating to latest distribute_setup.py
James Taylor
Merged in eivindgl/bx-python (pull request #2) fixed BinnedBitSet memory leak
eivindgl
fixed BinnedBitSet memory leak
mruffalo
lrucache.py: remove functools.total_ordering call This isn't present in Python 2.4, so replace it with a manual total ordering by implementing the rest of the __comparison__ methods.
mruffalo
lrucache.py: remove __future__.generators import Python 2.4 is now the minimum version, and generators don't require a __future__ import now.
olgert denas
BED4 output (bnMapper) had a problem
olgert denas
progress message / chromosome
olgert denas
check cached chains are up to date and int chain score
olgert denas
fixed small bugs and added options
olgert denas
fixed issue with peaks spanning multiple chains
olgert denas
scripts for chain to EPO (.out) conversion and feature mapping
jsilter
Alter bbi_file.pyx ZoomLevel._summary_blocks_in_region to be slightly more efficient. Should skip reading data when chrom_id doesn't match equery
mruffalo
If Python 3, use 2to3 distutils builder instead
mruffalo
pstat.py: fix one cmp call, add TODO to another
mruffalo
Fix more usage of old cmp function Conflicts: lib/bx/gene_reader.py lib/bx_extras/lrucache.py
mruffalo
phylo.newick: fix old usage of cmp, __cmp__ These are removed in Python 3. Use __lt__ and __eq__, and fill in the rest with functools.total_ordering
mruffalo
intervals/intersection.pyx: replace old 'cmp' usage This function no longer exists in Python 3. Replace __cmp__ with a total ordering: __eq__, __lt__, __gt__, __le__, __ge__
mruffalo
setup.py: correctly identify Python 3 as >= 2.4 for issue #35
mruffalo
Raise exceptions instead of raw strings for issue #35
James Taylor
Cythonizing everything with 15.1, fix some deprecations and tests. AlignmentMappingTests currently segmentation faults, but other tests look good
James Taylor
BigWig/BigBed: fixed some missing type declerations in the summarization code (~20 times faster)
James Taylor
Update .c from .pyx
James Taylor
BigWig/BigBed: fix a bug where data might not be returned for summary blocks spanning chromosome boundaries
James Taylor
James Taylor
Helper for displaying progress bar while iterating
Nate Coraor
Fixes to allow BGZF to compile on Solaris
Kanwei Li
Add back BGZF tests
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