Ron Levine 36c27155af Made the threshold for the probability of a state being active a command line argument ... remove TODO comment after activeProbThreshold recover static ACTIVE_PROB_THRESHOLD for unit tests Add min/max values for active_probability_threshold parameter Move activeProbThreshold parameter to GATKArguemtnCollection define ACTIVE_PROB_THRESHOLD in unit tests add construction of argCollection in in ctor Move arguments from GATKArgumentCollection to ActiveRegionWalker Throw exception if threshold < 0 or > 1 in ActivityProfile ctor max propogation distance parameter to ActiveRegionWalker for AcrtivityProfile Use polymorphic getMaxProbPropagationDistance() so BandPassActivityProfile computes the crrect region size cutoff Get the maxProbPropagationDistance from the super class's method, instead of directly, this is safer Removed extraneous command line imports and make maxProbPropagationDistance a hidden argument remove limit check for activeProbThreshold, not necessary because the check is made when imput as a command line arg Remove extra 'region' in the doxygen param description for maxProbPropagationDistance		2014-10-10 10:36:02 -04:00
..
gatk-package-distribution	Now passing in the path to the GATK directory to tests.	2014-09-02 01:40:59 +08:00
gatk-queue-extensions-distribution	Now passing in the path to the GATK directory to tests.	2014-09-02 01:40:59 +08:00
gatk-queue-package-distribution	Now passing in the path to the GATK directory to tests.	2014-09-02 01:40:59 +08:00
gatk-tools-protected	Made the threshold for the probability of a state being active a command line argument	2014-10-10 10:36:02 -04:00
pom.xml	Update pom versions to mark the start of GATK 3.3 development	2014-07-17 12:09:33 -04:00