Commits

Author Commit Message Labels Comments Date
James Taylor
Fixed a bug in count_range for BinnedBitset Added bed_coverage, bed_intersect, and bed_merge_overlapping (all using binned bitsets)
James Taylor
C implementation of binned bitsets.
James Taylor
Added a script for extracting the regions covered (in the reference species) by all other species in an alignment.
James Taylor
Fixed off by one error in intervals.Intersecter Added a function to BinnedBitSet for counting the number of set bits in a ranges
Bob Harris
stub module that eventually will read/write LAV format alignment blocks with same interface as maf.py and axt.py
Bob Harris
(1) corrected reverse_complement (2) brought axt support up-to-snuff with maf (3) which necessitated changes to maf and core (4) added stubs for lav
James Taylor
"bed_merge_overlapping" merges all overlapping intervals in a bed file. It uses projection onto a bitset like featureBits, but the bitset is broken up into bins which makes things much faster for smaller data sets.
James Taylor
Forgot the cookbook package. Fixed bitset.pyx (still in progress) so that it builds.
James Taylor
Importing everything
James Taylor
Making trunk directory
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