Mark DePristo 5bcb5c7433 Preliminary refactoring of ART ... -- Refactored ART into clearer, simpler procedures. Attempted to merge shared code into utility classes. -- Added some docs -- Created a new, testable ActivityProfile that represents as a class the probability of a base being active or inactive -- Separated band-pass filtering from creation of active regions. Now you can band pass filter a profile to make another profile, and then that is explicitly converted to active regions -- Misc. utility functions in ActiveRegionWalker such as hasPresetActiveRegions() -- Many TODOs in ActivityProfile.		2012-03-14 17:26:37 -04:00
..
R	GATKReport v1.0	2012-03-12 23:09:19 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Preliminary refactoring of ART	2012-03-14 17:26:37 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2012-03-13 09:28:16 -04:00
testdata	analyzeRunReports cleanup for new minimal GATKRunReport structure	2012-03-12 09:46:26 -04:00