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Author Commit Message Labels Comments Date
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
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
Kanwei Li
Use instanceof() instead of type()
James Taylor
add bed_extend_to.py, extend each record to a minimum size
James Taylor
Merge to restore BGZFFile
James Taylor
Backed out changeset c1e165e97419, bgzf is still useful.
James Taylor
bigbed support
James Taylor
script for computing signal profiles (from bigwig) around interval centers
James Taylor
small bigwig tweaks
James 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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