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
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extensions/gatk	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
function	No more "Q-<pid>@<host>". Generated log file names now use the first output + ".out" (ex. my.vcf.out) or the name of the first QScript plus the order the function was added (ex. MyScript-1.out). The same function added twice with the same outputs will now have the same default logs, meaning the 2nd instance of the function won't be added to the graph twice.	2012-01-08 12:11:55 -05:00
pipeline	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
util	No more "Q-<pid>@<host>". Generated log file names now use the first output + ".out" (ex. my.vcf.out) or the name of the first QScript plus the order the function was added (ex. MyScript-1.out). The same function added twice with the same outputs will now have the same default logs, meaning the 2nd instance of the function won't be added to the graph twice.	2012-01-08 12:11:55 -05:00