Commits

Author Commit Message Labels Comments Date
mruffalo
lrucache.py: remove functools.total_ordering call
mruffalo
lrucache.py: remove __future__.generators import
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
mruffalo
phylo.newick: fix old usage of cmp, __cmp__
mruffalo
intervals/intersection.pyx: replace old 'cmp' usage
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
Kanwei Li
Fix bigBed#query
Kanwei Li
typo
Brad Chapman
Add manifest to pull in generated C files; eases easy_install/pip installations; closes issue #21
Brad Chapman
Support space separated files as backup to tab separation with allow_spaces flag; closes issue #27
Kanwei Li
Tests now run when PYTHONPATH is not set
Kanwei Li
Remove bigbed_file.so
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