gatk3的最后一个经典版本3.8

Mark DePristo 233f70f8ba Final cleanup of TraversalProgressMeters, moved to utils.progressmeter ... -- TraversalProgressMeter now completely generalized, named ProgressMeter in utils.progressmeter. Now just takes "nRecordsProcessed" as an argument to print reads. Completely removes dependence on complex data structures from TraversalProgressMeter. Can be used to measure progress on any task with processing units in genomic locations. -- a fairly simple, class with no dependency on GATK engine or other features. -- Currently only used by the TraversalEngine / MicroScheduler but could be used for any purpose now, really.		2012-09-10 20:14:14 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	Bug fix in HC GenotypingEngine to ensure that all the merged complex events get properly added to the priority list used by VariantContextUtils when combining multiallelic events.	2012-09-09 13:47:54 -04:00
public	Final cleanup of TraversalProgressMeters, moved to utils.progressmeter	2012-09-10 20:14:14 -04:00
settings	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00
.gitignore	a few more useful git ignores	2012-09-01 11:08:36 -04:00
build.xml	More memory for gatkdocs and extracthelp targets	2012-09-05 15:45:22 -04:00
ivy.xml	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00