-- Minor refactoring to allow LocusScatterFunction to have maxIntervals be the original scatter count, rather than capping this by the interval count as Contig and Interval do
-- scatterLocusIntervals master utility
-- Moved around some general functionality from GenomeLocSortedSet to GenomeLoc
-- Util function for reversing a list (List<T> -> List<T>, unlike Collections version)
-- DoC is PartitionType.INTERVAL
-- Significant unit tests on new functionality (all passing)
-- Ready for real-world testing, as soon as I can get LocusScatterFunction.scala to actually work
-- Added PartitionType.READ, and associated ReadScatterFunction. ReadScatterFunction is literally just ContigScatterFunction until someone wants to implement something better
-- LocusWalkers (and subclasses RodWalkers and RefWalkers) are by default PartitionType.LOCUS.
Moved gsalib and queueJobReport.R to embeddable namespaced locations.
Updated packager dependencies/dir to add an @includes which filters the embedded fileset.
RScriptExecutor can now JIT compiles the gsalib.
RScriptExecutor uses ProcessController and sends the Rscript output to java's stdout when run under -l DEBUG.
Refactored ProcessController and IOUtils from Queue to Sting Utils.
Added more unit tests to ProcessController along with a utility class to hard stop OutputStreams at a specified byte count.
Replaced uses of some IOUtils with Apache Commons IO.
ShellJobRunner refactored to use direct ProcessController and now kills jobs on shutdown.
Better QGraph responsiveness on shutdown by using Object.wait() instead of Thread.sleep().
-- General purpose RScript executor in java (please use when invoking RScripts)
-- Removed groupName. This is now analysisName
-- Explicitly added capability to enable/disable individual QFunction
*Added the functions to turn a BLASR generated BAM file into a usable BAM file.
*Modified the bwa parameters according to test results from NA12878 pb2k dataset.
-- onExecutionDone(Map(QFunction, JobRunInfo)) is the new signature, so that you can walk over your jobs and inspect their success/failure and runtime characteristics
-- This function is called when the Qscript ends, so scripts can overload this function if they want to run some code after all of the jobs have completed
- Ability to pass a different resident memory reservation and limits. Useful for large pileups of low pass genome data that sometimes need high -Xmx6g but usually don't exceed 2-3g in actual heap size.
- Fixed jobPriority to work for all job runners. Now must be a integer between 0 and 100- even for GridEngine- and will be mapped to the correct values.
- Passing parallel environment and job resource requests to LSF and GridEngine. Useful for passing tokens like iodine_io=1 and -pe pe_slots 8
- Refactored GridEngine JobRunner to also provide basic support for other job dispatchers with DRMAA implementations such as Torque/PBS. Should work for basic running but advanced users must pass their own jobNativeArgs from the command line or in customized QScripts until someone maps properties like jobQueue, jobPriority, residentRequest, etc. into a Torque/PBS/etc. dispatcher.
Mark DePristo
Khalid Shakir
Eric Banks
Mauricio Carneiro
Menachem Fromer