Author Commit Message Labels Comments Date
Default avatar Ian Schenk
Added base coverage and coverage operations.
Default avatar Ian Schenk
fixed an error where an entire chromosome could be missed.
Bob Harris avatarBob Harris
introductory LAV support
Bob Harris avatarBob Harris
removing some debug prints
Bob Harris avatarBob Harris
specific sequence formats are now subclasses of SeqFile, which provides common functionality like reverse-complement
Default avatar Ian Schenk
small change in merge.py
Default avatar Ian Schenk
Added subtract and merge, updated intersect and __init__
James Taylor avatarJames Taylor
Add C files so pyrex not needed to build (still a good idea...)
Default avatar David King
fixed import statements for pwm libs
Bob Harris avatarBob Harris
added fasta format
Bob Harris avatarBob Harris
sequence formats have a commonality now, like alignment formats (will add fasta later)
Bob Harris avatarBob Harris
paths to sample files now (allegedly) platform independent
Bob Harris avatarBob Harris
sample file for qdna_tests
Bob Harris avatarBob Harris
added qdna_tests.py
Bob Harris avatarBob Harris
support for quantum DNA files
Bob Harris avatarBob Harris
has been renamed to nib_tests.py
Bob Harris avatarBob Harris
added nib_tests.py
Bob Harris avatarBob Harris
(used to be test_nib.py), updated for inclusion with other bx tests
Bob Harris avatarBob Harris
wasn't looking in correct path for support modules
Bob Harris avatarBob Harris
documentation conformity
Bob Harris avatarBob Harris
axt writer incorrectly assumed score is an integer
Default avatar Ian Schenk
New intersect operation, hopefully for real this time.
Default avatar Ian Schenk
New intersect operation along with modifications to io, etc.
James Taylor avatarJames Taylor
Stuff, some support for maf i and e rows, a new tiling script.
Default avatar David King
added some *more* annotation checks to gene_reader.FeatureReader\
Default avatar David King
added bitset_interval_intersect to utils
Default avatar David King
gene_reader.py uses bitset_utils now
Default avatar David King
bitset_utils.py: some cleanup
James Taylor avatarJames Taylor
Another script I had in several places so it is probably
Default avatar David King
name change
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