Commits

Author Commit Message Labels Comments Date
David King
change empty zeros (numpy) to int for counts
David King
Remove all-gap columns after removing rows of the alignment
James Taylor
Clean up checking for valid blocks, if there were empty components the whole block was skipped, now those components are just removed.
James Taylor
Generated C code for twobit.
Bob Harris
make score a number only if it's a string
Bob Harris
make score a number if at all possible
Bob Harris
corrected species_to_lengths when contigs occur
chinmay
Bug fix in concat.py
Bob Harris
lav header can contain sequence names with extra stuff like (reverse complement), truncating for the sake of maf and everything else downstream
Bob Harris
updated test to match change in lav.py
Bob Harris
changed acquisition of src (species.chrom) to check h-stanza first; this means that if the aligned sequence was fasta and had a header, we fetch src from there instead of attempting to reconstruct it from the path
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
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