Author Commit Message Labels Comments Date
James Taylor avatarJames Taylor
Fixes noticed by Bob.
James Taylor avatarJames Taylor
Scoring now handle alignments, including multiple. Should be exactly the
James Taylor avatarJames Taylor
Basic module for scoring pairwise alignments.
Bob Harris avatarBob Harris
changed binBitsSetRange to leave ALL_ONE bins as is; may reduce memory footprint when long ranges are set (longer than a bin)
James Taylor avatarJames Taylor
Switched from distutils to setuptools.
James Taylor avatarJames Taylor
Merging David's changes from universe version of this file.
James Taylor avatarJames Taylor
Added "bed_subtract_basewise" tool and fixed some bugs in and/or for
Default avatar David King
Average was getting nan when sum < 0. Now it checks the denominator.
James Taylor avatarJames Taylor
Binned arrays can now be written to a file. Only the bins that are
Bob Harris avatarBob Harris
line counting was incorrect
James Taylor avatarJames Taylor
Remove some dead code from bed_complement.py
James Taylor avatarJames Taylor
Added:
Bob Harris avatarBob Harris
making them more pythonic
Bob Harris avatarBob Harris
making it more pythonic
Bob Harris avatarBob Harris
score argument was being ignored
Bob Harris avatarBob Harris
Bob Harris avatarBob Harris
Bob Harris avatarBob Harris
added caller-supplied species names
Bob Harris avatarBob Harris
changed import paths to bx...
Bob Harris avatarBob Harris
changed import of interval_index_file
James Taylor avatarJames Taylor
Binned bitsets now use two sentinals, ALL_ONE for bins containing all ones and ALL_ZERO for bins containing all zeros. Boolean operations (and, or, not) implemented (with tests).
James Taylor avatarJames Taylor
Undo path change, need to make this more easily configurable
James Taylor avatarJames Taylor
Added tests for Bitset and BinnedBitset covering set/clear, setrange, countrange, next_set/next_clear
Bob Harris avatarBob Harris
completion of yesterday's correction; incorporating other 'lost' changes (which consists only of a comment)
James Taylor avatarJames Taylor
More import fixes
James Taylor avatarJames Taylor
Allow bed_merge_overlapping to take input from both stdin and files
Bob Harris avatarBob Harris
Added species_to_lengths argument to Alignment constructor.
James Taylor avatarJames Taylor
Another bug fix for counting in binned bitsets
James Taylor avatarJames Taylor
Fixed a bug in count_range for BinnedBitset
James Taylor avatarJames Taylor
C implementation of binned bitsets.
  1. Prev
  2. Next
Help
Tip: Filter by directory path e.g. /media app.js to search for public/media/app.js.
Tip: Use camelCasing e.g. ProjME to search for ProjectModifiedEvent.java.
Tip: Filter by extension type e.g. /repo .js to search for all .js files in the /repo directory.
Tip: Separate your search with spaces e.g. /ssh pom.xml to search for src/ssh/pom.xml.
Tip: Use ↑ and ↓ arrow keys to navigate and return to view the file.
Tip: You can also navigate files with Ctrl+j (next) and Ctrl+k (previous) and view the file with Ctrl+o.
Tip: You can also navigate files with Alt+j (next) and Alt+k (previous) and view the file with Alt+o.