Commits

Author Commit Message Labels Comments Date
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
Kanwei Li
Use deque instead of list comprehension to greatly increase performance
Kanwei Li
Rename bx.intervals.random to bx.intervals.random_intervals so it doesn't clobber python namespace. This fixes unit test for intersection_tests.py and all tests are green now.
Kanwei Li
Remove unused bgzf test data
Kanwei Li
Add BigWig tests and test datasets. Fix error with min and max values being switched. Fix issue with fetching from full.
Kanwei Li
Make mean, max and min return NaN if no values in the region instead of 0.0. Move bigWig specific code back to bigwig_file.pyx. More error checking
Kanwei Li
Fully working and correct bigWig reader. Added new 'query' method that is used to return 'summary_size' number of dictionaries containing the mean, max, min, coverage, and std_dev.
James Taylor
Fixes to bigwig stuff from Bob Harris
James Taylor
BigWigFile subclassing BBIFile, support for creating summaries from 'unzoomed' data points.
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