Commits

Author Commit Message Labels Comments Date
James Taylor
Even more pythonic.
James Taylor
Pythonic interface to twoBit files.
James Taylor
Pyrex code for twoBit files.
James Taylor
Read only twoBit support. Not yet using the SeqFile interface because I'm not sure how to make it fit a file that can contain many sequences. We probably need a "SeqCollection" interface, with an implementation for this, fasta, and a "directory full of nib files".
Bob Harris
removed a couple unused variables that I should have removed last week
Bob Harris
corrected use of lookahead buffer
James Taylor
Update to lates ez_setup.py, add generated code for _nib.pyx
Ian Schenk
Added a wrapper for GenomicIntervalReader that skips lines that throw ParseError. This was moved here from galaxy.
James Taylor
Okay, but lets find the windows that AREN'T in gaps (sheesh)
James Taylor
Fix.
James Taylor
Not sure random is really a benefit here (since it is uniform and approaches evenly anyway).
James Taylor
Script for building a bed file of windows over some set of regions.
Bob Harris
collapsed basic_fetch into raw_fetch (layering no longer needed or useful)
Bob Harris
further improvements, about 15% faster
James Taylor
Byte unpacking loop is by far the slowest part of reading NIB data, now implemented in Pyrex.
Bob Harris
Removing the sys.stdout change from this test
Bob Harris
Removing the sys.stdout change from this test
Bob Harris
Removing the sys.stdout change from this test
Bob Harris
Removing the sys.stdout change from this test
James Taylor
Removing the sys.stdout change from these tests (it can cause crashed, and nose can already deal with this by capturing output printed by tests and notifying.
Bob Harris
this has been moved to test_data/seq_tests
Bob Harris
this has been moved to test_data/seq_tests
Bob Harris
this has been moved to test_data/seq_tests
Bob Harris
this has been moved to test_data/seq_tests
Bob Harris
moved test data for bx.seq tests to common area
Bob Harris
moved test data for bx.seq tests to common area
Bob Harris
moved test data for bx.seq tests to common area
Bob Harris
moved test data for bx.seq tests to common area
Ian Schenk
intervals.io now throws a ParseError is start > end. This should avoid seg faults with bitsets too.
Bob Harris
moving test data for bx.seq tests to common area
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