Mark DePristo 9eec33ec3b Complete GSA-497: Let Queue write out runInfo on the fly, after each job group finishes running ... -- Queue will incrementally now write out its jobReport.txt file whenever jobs finish running (FAIL or DONE) -- This makes it far easier to track what's going on, or to analyze incrementally performance results coming out of Queue -- Generally cleaned up the QJobsReporting code, creating a new clean class QJobsReporter that holds all of the information on what to do log and where to put into, which was previously scattered in QCommandLine and QJobReport		2012-08-21 14:44:18 -04:00
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engine	Complete GSA-497: Let Queue write out runInfo on the fly, after each job group finishes running	2012-08-21 14:44:18 -04:00
extensions	Pass the original GATK unsafe parameter to the VcfGatherFunction	2012-07-02 16:03:11 -04:00
function	Added setupRetry() to modify jobs when Queue is run with '-retry' and jobs are about to restart after an error.	2012-08-13 15:43:05 -04:00
library	Fix edge case for very small VCFs	2012-01-19 00:51:28 -05:00
util	Complete GSA-497: Let Queue write out runInfo on the fly, after each job group finishes running	2012-08-21 14:44:18 -04:00
QCommandLine.scala	Complete GSA-497: Let Queue write out runInfo on the fly, after each job group finishes running	2012-08-21 14:44:18 -04:00
QException.scala	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
QScript.scala	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
QScriptManager.scala	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
QSettings.scala	Changed the default memory limit from none to 2GB upon suggestions from delangel, carneiro, and depristo.	2012-08-20 21:41:13 -04:00