Commits

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Author Commit Message Labels Comments Date
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
James Taylor
refactor bigwig support, add more tests
James Taylor
Fix 'first line is header' support in tabular.io
Daniel Blankenberg
Remove leading and trailing white space from around chromosome names in GenomicInterval class.
James Taylor
Fix for fixed step records in bigwig
Kanwei Li
Free tree iterator in clustertree after getting results
Kanwei Li
Bump to 0.7.0, fix doc URL
Kanwei Li
Fix string padding in bbi.bpt_file. Fix edge case when valid_count was less than 1, causing a division by zero
Kanwei Li
Minor refactorings to bbi
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