VCF gathering passes on the no_header and sites_only flags to CombineVariants.
Fixed deletion of gathered log files. Although they are intermediate and do not need to be re-run if not present, they should not be deleted.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5508 348d0f76-0448-11de-a6fe-93d51630548a
JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar.
JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar.
Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath.
Walkers from the GATK package are now also embedded into the Queue package.
Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP.
Removed the GATK jar argument from the example QScripts.
Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts:
1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers.
2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3
Removed other unused code.
Re-fixed dry run function ordering.
Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
Fixed initialization of pending counts when using -startFromScratch so the count doesn't start at zero and end at -<#njobs>.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5483 348d0f76-0448-11de-a6fe-93d51630548a
- LSF recycles memory for C arrays, but sets a separate variable setting the size of the array to zero.
- JNA only sees the non-NULL pointer and starts to auto-access it, sometimes causing a SIGSEGV.
- In the short term neutered the jobInfoEnt structure so that this bad array is not autoRead().
QGraph updates:
- Job status is now checked in bulk every 30 seconds instead of one job at a time, even in the middle of dispatching jobs.
- If there is a hiccup (unexpected but not fatal error) during status check then the the error is ignored and status is checked again 30 seconds later.
- Jobs prefer to dispatch depth vs. breadth first.
More refactoring of SG framework separating the reusable code from the implementations.
The DistributedScatterFunction is still a work in progress and is not enabled yet. Still need to think through how Queue handles when a job dies.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5387 348d0f76-0448-11de-a6fe-93d51630548a
More refactoring to do so that other new scatter functions can be implemented very easily and annotated on walkers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5363 348d0f76-0448-11de-a6fe-93d51630548a
Moved the BamListWriter from FCP to ListWriterFunction in the Queue core.
Added an ExampleCountLoci QScript along with an example pipeline integration test which checks MD5s.
Added a few more utility methods to PipelineTest including a currentGATK variable that points to the GATK jar.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5121 348d0f76-0448-11de-a6fe-93d51630548a
Updated the Queue scatter/gather for read walkers to include -L unmapped on the last scatter job when intervals aren't specified, and to map it correctly when it is explicitly set.
Simplified the build.xml/ivy.xml to fix a bug reported with "ant clean dist test" where the scalac target wasn't found.
Now building all scala code at the same time, just like all java code is compiled at the same time.
Sped up the build for everyone by uncommenting a small bit of classes so that javac/scalac will not constantly launch trying to build .class files that will never compile.
Moved some source files to their expected location so that the .java/.scala -> .class is a one-to-one match, again keeping the compilers from wasting cycles.
Used <uptodate> and <touch> to skip extracting the help text and generating the GATK Queue extensions when the source files haven't been modified.
Fixed a couple errors when the <javadoc> task is run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4963 348d0f76-0448-11de-a6fe-93d51630548a
Added an initial test for genotyping chr20 on ten 1000G bams.
Since tribble needs logging support too, for now setting the logging level and appending the console logger to the root logger, not just to "org.broadinstitute.sting".
Updated IntervalUtilsUnitTest to output to a temp directory and not the SVN controlled testdata directory.
Added refseq tables and dbsnps to validation data in BaseTest.
Now waiting up to two minutes for gather parts to propagate over NFS before attempting to merge the files.
Setting scatter/gather directories relative to the -run directory instead of the current directory that queue is running.
Fixed a bug where escaping test expressions didn't handle delimiters at the beginning or end of the String.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4717 348d0f76-0448-11de-a6fe-93d51630548a
Removed obsolete usages of PackageUtils with updated PluginManager.
Ported Queue interval utilities written in scala over to Sting's java IntervalUtils.
Added a very basic intergration test to ensure that the fullCallingPipeline.q compiles.
Added options to specify the temporary directories without having to use -Djava.io.tmpdir (useful during the above integration test).
While adding tempDir added options to specify the run directory from the command line, for example "-runDir v1".
Upgraded to scala 2.8.1 and updated calls to deprecated functions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4661 348d0f76-0448-11de-a6fe-93d51630548a
for anything that needs to be simultaneously aware of multiple references, eg
Queue's interval sharding code, liftover support, distributed GATK etc.
GenomeLocParser instances must now be used to create/parse GenomeLocs.
GenomeLocParser instances are available in walkers by calling either
-getToolkit().getGenomeLocParser()
or
-refContext.getGenomeLocParser()
This is an intermediate change; GenomeLocParser will eventually be merged
with the reference, but we're not clear exactly how to do that yet. This
will become clearer when contig aliasing is implemented.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4642 348d0f76-0448-11de-a6fe-93d51630548a
When the cleaner interval scatter count is set to one explicitly setting the intrevals to Nil.
TODO: Need to add an option that lets the user choose from the command line to scatter all contigs or just those in the intervals list. For now can get relatively the same behavior by setting the interval scatter count equal to the number of contigs+1, assuming the random contigs come at the end of the sequence dictionary.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4565 348d0f76-0448-11de-a6fe-93d51630548a
Added a brute force -retry <count> option to Queue for transient errors.
Waiting up to 2 minutes for the LSF logs to appear before trying to display the errors from the logs.
Updates to the local job runner error logging when a job fails.
Refactored QGraph's settings as duplicate code was getting out of control.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4563 348d0f76-0448-11de-a6fe-93d51630548a
- More cleanup including removing the temporary classes and intermediate error files. Quieting any errors using Apache Commons IO 2.0.
- Counting the contigs during the QScript generation instead of the end user having to pass a separate contig interval list.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4539 348d0f76-0448-11de-a6fe-93d51630548a
Queue GATK generated .intervals is now a List(File) again removing special case handling in the generator.
Instead of using @Scatter annotation, using ScatterFunction instance to determine if a job can be scattered.
Implemented special VcfGatherFunction which only uses the header from the first file, even if the other files differ in their headers.
Added a -deleteIntermediates to Queue to delete the outputs from intermediate commands after a successful run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4536 348d0f76-0448-11de-a6fe-93d51630548a
Queue now submits new LSF jobs only after previous functions have completed successfully.
When the Queue process is shutdown (ex: via Control-C) sends a bkill command for any running jobs.
Ported commands like creating directories and scatter/gather interval list to scala functions.
Updates to LSF status tracking by porting the python to internally generated bash scripts.
Temporarily disabled job name submission to LSF. Plus side is that the full command is now available in "bjobs -w". TODO: Put back jobName passing to LSF based on an option?
Changed BaseTest to allow scala to access paths to references.
Changed the extension generator to default the analysis name to the walker "name".
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4442 348d0f76-0448-11de-a6fe-93d51630548a
No longer generating deprecated GATK arguments on the Queue extensions.
Emitting deprecation warnings to Queue compile to help debugging issues.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4195 348d0f76-0448-11de-a6fe-93d51630548a
Added an example of using a walker with Queue and a custom -classpath.
Removed an unused import statement in NamedFileWrapper.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4143 348d0f76-0448-11de-a6fe-93d51630548a
To add support for "-I:tumor tumor.bam", the GATK argument
import_file (-I) is now generated as a List of NamedFile objects.
Could not get sugar working 100%. To activate sugar import the
gatk package. This effectively adds a new method to java.io.File
called toNamedFile. When adding a file to the list call
countReads.import_file :+= myJavaFile.toNamedFile
See scala/qscript/examples for actual examples.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4122 348d0f76-0448-11de-a6fe-93d51630548a
Added the a CommandLineFunction.jobDependencies that will explicitly force a function to wait for a file, even if the value isn't otherwise listed on an @Input.
More bug fixes and refactoring of functions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4048 348d0f76-0448-11de-a6fe-93d51630548a
Some refactoring of Queue extensions for reusability in scripts.
Putting the extensions into the Queue.jar after building them.
More updates to GATK walker arguments specifying @Input and @Output for Queue.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4032 348d0f76-0448-11de-a6fe-93d51630548a
Changes to StingUtils command line for use in Queue, replacing Queue's use of property files.
Updates to walkers used in existing QScripts to add @Input/@Output.
RMD used in @Required/@Allows now has a new default equal to "any" type.
New QueueGATKExtensions.jar generator for auto wrapping walkers as Queue CommandLineFunctions.
Added hooks to modify the functions that perform the Scattering and Gathering (setting their jar files, other arguments, etc.)
Removed dependency on BroadCore by porting LSF job submitter to scala.
Ivy now pulls down module dependencies from maven.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3984 348d0f76-0448-11de-a6fe-93d51630548a
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