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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
..
VectorPairHMM Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -04:00
c After renaming the packages, instead of updating the JNI library used for testing bwa, moving the classes to the archive. 2014-05-19 17:36:41 -04:00
chainFiles The contig is named MT not M in b36. Delivers PT68890442. 2014-04-08 10:03:47 -04:00
doc Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
external-example Various fixes for package tests. 2014-09-04 15:30:31 -04:00
gatk-engine Now passing in the path to the GATK directory to tests. 2014-09-02 01:40:59 +08:00
gatk-queue Now passing in the path to the GATK directory to tests. 2014-09-02 01:40:59 +08:00
gatk-queue-extensions-generator Moved arguments controlling options in output files into the engine 2014-09-05 21:18:11 -04:00
gatk-queue-extensions-public Moved arguments controlling options in output files into the engine 2014-09-05 21:18:11 -04:00
gatk-root Added -writeFullFormat engine-level argument 2014-09-17 08:25:27 -04:00
gatk-tools-public Made the threshold for the probability of a state being active a command line argument 2014-10-10 10:36:02 -04:00
gatk-utils Now passing in the path to the GATK directory to tests. 2014-09-02 01:40:59 +08:00
gsalib Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -04:00
java/config Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
package-tests Various fixes for package tests. 2014-09-04 15:30:31 -04:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
repo Added -writeFullFormat engine-level argument 2014-09-17 08:25:27 -04:00
src/main/scripts/shell For now, executing the delete_maven_links.sh just ahead of creating the symbolic links during the process-test-resources phase. 2014-06-25 02:32:15 +08:00
pom.xml Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -04:00