gatk-3.8/public/java
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
..
config Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
src Preliminary refactoring of ART 2012-03-14 17:26:37 -04:00
test CountReadsInActiveRegions now emits a detailed GATK report 2012-03-14 17:26:37 -04:00