Commits

Author Commit Message Labels Comments Date
ajish
flank capitalization fixes
ajish
remerge with james_taylor
Kanwei Li
- Changes to array_tree to enable frequencies (how many times a node is visited, and also option to disable leaf nodes to save space
Brent Pedersen
add new ez_setup.py
James Taylor
Note about issue #10
Kanwei Li
Remove bgzf as it's no longer planned to be used
Brent Pedersen
add cython generated file to repo
James Taylor
Two fixes for align.tools from Thomas Mailund
James Taylor
Make BGZF test a real unittest
James Taylor
BGZF support (really simple wrapper to code from samtools)
Kanwei Li
Return empty list for interval operations on empty trees to prevent segfaults. Fixes #8
Kanwei Li
Update array_tree version assert, use cython for cluster
Kanwei Li
Fix interval_index_file test to use max parameter
Kanwei Li
Fix return bug in bits#bitCountRange
Kanwei Li
Added array_tree tests, bump to version 1
ajish
extract_genomic _dna can now use flank arguments -l N -r N
ajish
added and modified extract_genomic_dna.py -- to extract genomic regions from directories of fasta/nib files based on coordinates in a bed/gff whatever
ajish
rightWords major updates -- uses binom cdf to calc p-value
ajish
bug-fix for improper control set use -- if word in query is not found in background pvalue is -1
ajish
rightwordmine prints wordfilename even with no background set
ajish
updated rightwordmine to allow no background file.
ajish
fix back to bx-python
ajish
tweaks
ajish
updated setup.py to reflect new package name -- bx-omelogic
ajish
many changes -- added the initial version of rightwordmine (commodus)
ajish
Changes all over
ajish
Added test sets for interval operations
ajish
Making the interval comparisons strand specific and fractional
guru
Bug fix in gops concatenation: previously it was returning 1 less column from the 2nd dataset in cases where 2nd dataset had more columns than 1st dataset.
Kanwei Li
Make wiggle parsing more resiliant (fix UCSC truncation issues)
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