4 Commits (dac3958461173a38a1bfad03343cd1782b3a3628)

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
Khalid Shakir	89a581a66f	Added ability to specify arguments in files via -args/--arg_file ... Pushing back downsample and read filter args so they show up in getApproximateCommandLineArgs()	2011-10-24 15:58:34 -04:00
Mark DePristo	9992c373be	Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.	2011-07-17 20:29:58 -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