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Author Commit Message Labels Comments Date
jsilter avatarjsilter
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 avatarmruffalo
If Python 3, use 2to3 distutils builder instead
mruffalo avatarmruffalo
pstat.py: fix one cmp call, add TODO to another
mruffalo avatarmruffalo
Fix more usage of old cmp function
mruffalo avatarmruffalo
phylo.newick: fix old usage of cmp, __cmp__
mruffalo avatarmruffalo
intervals/intersection.pyx: replace old 'cmp' usage
mruffalo avatarmruffalo
setup.py: correctly identify Python 3 as >= 2.4 for issue #35
mruffalo avatarmruffalo
Raise exceptions instead of raw strings for issue #35
James Taylor avatarJames Taylor
Cythonizing everything with 15.1, fix some deprecations and tests. AlignmentMappingTests currently segmentation faults, but other tests look good
James Taylor avatarJames Taylor
BigWig/BigBed: fixed some missing type declerations in the summarization code (~20 times faster)
James Taylor avatarJames Taylor
Update .c from .pyx
James Taylor avatarJames Taylor
BigWig/BigBed: fix a bug where data might not be returned for summary blocks spanning chromosome boundaries
James Taylor avatarJames Taylor
James Taylor avatarJames Taylor
Helper for displaying progress bar while iterating
Nate Coraor avatarNate Coraor
Fixes to allow BGZF to compile on Solaris
Kanwei Li avatarKanwei Li
Add back BGZF tests
Kanwei Li avatarKanwei Li
Fix bigBed#query
Kanwei Li avatarKanwei Li
typo
Brad Chapman avatarBrad Chapman
Add manifest to pull in generated C files; eases easy_install/pip installations; closes issue #21
Brad Chapman avatarBrad Chapman
Support space separated files as backup to tab separation with allow_spaces flag; closes issue #27
Kanwei Li avatarKanwei Li
Tests now run when PYTHONPATH is not set
Kanwei Li avatarKanwei Li
Remove bigbed_file.so
Kanwei Li avatarKanwei Li
Use instanceof() instead of type()
James Taylor avatarJames Taylor
add bed_extend_to.py, extend each record to a minimum size
James Taylor avatarJames Taylor
Merge to restore BGZFFile
James Taylor avatarJames Taylor
Backed out changeset c1e165e97419, bgzf is still useful.
James Taylor avatarJames Taylor
bigbed support
James Taylor avatarJames Taylor
script for computing signal profiles (from bigwig) around interval centers
James Taylor avatarJames Taylor
small bigwig tweaks
James Taylor avatarJames Taylor
Implement support for getting raw data points from bigwig, either in a numpy array or a list of start, end, val tuples
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