6 Commits (dea049553adc30bbf78f3df18f3f39009754fe02)

Author	SHA1	Message	Date
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
Eric Banks	0ca7428e76	Allow processing of empty intervals, but warn user when this case is encountered.	2011-10-28 12:12:14 -04:00
Eric Banks	ccfd853b34	Added further integration tests for rod-based intervals that deal with more complex cases. Good call by Mark to test the empty VCF example because we were failing on it; fixed.	2011-10-27 20:43:50 -04:00
Eric Banks	3273c20c98	Added integration tests for Tribble-based intervals and fixed up some of the other tests based on some method changes.	2011-10-26 15:29:18 -04:00
David Roazen	f18fffd625	Fixing broken paths to the testdata directory throughout the codebase.	2011-06-29 17:36:47 -04:00
David Roazen	3c9497788e	Reorganized the codebase beneath top-level public and private directories, ... removing the playground and oneoffprojects directories in the process. Updated build.xml accordingly.	2011-06-28 06:55:19 -04:00