gatk3的最后一个经典版本3.8

Khalid Shakir 746a5e95f3 Refactored parsing of Rod/IntervalBinding. Queue S/G now uses all interval arguments passed to CommandLineGATK QFunctions including support for BED/tribble types, XL, ISR, and padding. ... Updated HSP to use new padding arguments instead of flank intervals file, plus latest QC evals. IntervalUtils return unmodifiable lists so that utilities don't mutate the collections. Added a JavaCommandLineFunction.javaGCThreads option to test reducing java's automatic GC thread allocation based on num cpus. Added comma to list of characters to convert to underscores in GridEngine job names so that GE JSV doesn't choke on the -N values. JobRunInfo handles the null done times when jobs crash with strange errors.		2012-06-27 01:15:22 -04:00
licensing	Remove old licensing	2012-04-25 12:23:08 -04:00
protected/java	Moving ReduceReads into protected	2012-06-25 17:01:33 -04:00
public	Refactored parsing of Rod/IntervalBinding. Queue S/G now uses all interval arguments passed to CommandLineGATK QFunctions including support for BED/tribble types, XL, ISR, and padding.	2012-06-27 01:15:22 -04:00
settings	Rev tribble to 110. Log is:	2012-06-26 15:28:32 -04:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
build.xml	ant fasttest: for when you just can't wait	2012-06-01 15:17:18 -04:00
ivy.xml	JEXL update	2012-06-21 15:17:21 -04:00