Removed some generics from PluginManager for now until able to figure out syntax for requesting explicit subclass.
QStatusMessenger uses a slightly more primitive Map[String, Seq[RemoteFile]] instead of Map[ArgumentSource, Seq[RemoteFile]].
Added an QCommandPlugin.initScript utility method for handling specialized script types.
The runtime of these tests is extremely variable -- sometimes they will complete almost instantly,
other times they will wait in an LSF queue for 5-10+ hours. Minimize timeout errors by setting the
timeout for these tests to the maximum of 10 hours.
In addition to outputs, inputs are passed to QStatusMessenger.done()
CloneFunction.cloneIndex has a new CloneFunction.cloneCount companion useful for display purposes.
Bringing in the following relevant changes:
* Fixes the indel realigner N-Way out null pointer exception DEV-10
* Optimizations to ReduceReads that bring the run time to 1/3rd.
Conflicts:
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
DEV-10 #resolve #time 2m
Changed ReflectionUtils.getGenericTypes' order of looking for @ClassType since the primitive generic wasn't completely erased, only changed to Object which is incorrect.
More fixes to @Arguments labeled as java.io.File via incorrect @Input annotation.
Put in a default undocumented implementation of @Argument doc() to match the one added to @Input.
QScripts will now generate remote versions of files if the caller has not already passed in remote versions (or the QScript replaces the passed in remote references... not good)
Instead of having yet another plugin, combined QStatusMessenger and RemoteFileConverter under general QCommandPlugin trait.
The *.bai.done file for the .bai file was written in the run directory instead of in the specified output directory.
Changing getName() to getAbsolutePath() fixes this.
Signed-off-by: Joel Thibault <thibault@broadinstitute.org>
-- 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
Implemented a mixin called "RetryMemoryLimit" which will by default double the memory.
GridEngine memory request parameter can be selected on the command line via '-resMemReqParam mem_free' or '-resMemReqParam virtual_free'.
Java optimizations now enabled by default:
- Only 4 GC threads instead of each job using java's default O(number of cores) GC threads. Previously on a machine with N cores if you have N jobs running and java allocates N GC threads by default, then the machines are using up to N^2 threads if all jobs are in heavy GC (thanks elauzier).
- Exit if GC spends more than 50% of time in GC (thanks ktibbett).
- Exit if GC reclaims lest than 10% of max heap (thanks ktibbett).
Added a -noGCOpt command line option to disable new java optimizations.
Eric Banks
Mauricio Carneiro
kshakir
David Roazen
Guillermo del Angel
Ryan Poplin
Ami Levy Moonshine
Kristian Cibulskis
Johan Dahlberg
Mark DePristo
Joel Thibault