Commits

Author Commit Message Labels Comments Date
James Taylor
Added a method for accumulating scores along an alignment
Bob Harris
made gap/gap be ignored, and neighboring gaps on opposite strands incur two gap open penalties
James Taylor
Fixes noticed by Bob.
James Taylor
Scoring now handle alignments, including multiple. Should be exactly the
James Taylor
Basic module for scoring pairwise alignments.
Bob Harris
changed binBitsSetRange to leave ALL_ONE bins as is; may reduce memory footprint when long ranges are set (longer than a bin)
James Taylor
Switched from distutils to setuptools.
James Taylor
Merging David's changes from universe version of this file.
James Taylor
Added "bed_subtract_basewise" tool and fixed some bugs in and/or for
David King
Average was getting nan when sum < 0. Now it checks the denominator.
James Taylor
Binned arrays can now be written to a file. Only the bins that are
Bob Harris
line counting was incorrect
James Taylor
Remove some dead code from bed_complement.py
James Taylor
Added:
Bob Harris
making them more pythonic
Bob Harris
making it more pythonic
Bob Harris
score argument was being ignored
Bob Harris
Bob Harris
Bob Harris
added caller-supplied species names
Bob Harris
changed import paths to bx...
Bob Harris
changed import of interval_index_file
James Taylor
Binned bitsets now use two sentinals, ALL_ONE for bins containing all ones and ALL_ZERO for bins containing all zeros. Boolean operations (and, or, not) implemented (with tests).
James Taylor
Undo path change, need to make this more easily configurable
James Taylor
Added tests for Bitset and BinnedBitset covering set/clear, setrange, countrange, next_set/next_clear
Bob Harris
completion of yesterday's correction; incorporating other 'lost' changes (which consists only of a comment)
James Taylor
More import fixes
James Taylor
Allow bed_merge_overlapping to take input from both stdin and files
Bob Harris
Added species_to_lengths argument to Alignment constructor.
James Taylor
Another bug fix for counting in binned bitsets
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