svn's logs:
- Copied BAM indexing engine from Picard back into the GATK anticipating
shard merging algorithm. Tried to leave most of the building blocks in
Picard. If this turns into a logistical nightmare, I'll merge the building
blocks into the GATK as well.
- Reorganized the org.broadinstitute.sting.gatk.datasources package, giving
better separation of query and management functionality for reads, ref, rmd,
and samples.
- Merged Shard building blocks into org.broadinstitute.sting.gatk.datasources.
reads package, indicating it's current strong relationship with the reads,
rather than the general unifying element I wish this would be.
- Collapsed BAMFormatAwareShard into Shard.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5184 348d0f76-0448-11de-a6fe-93d51630548a
Updated LibBatIntegrationTest to use proper networked temp directory accessible by local machines and nodes.
Disabling the FCPTest until the VE3 is incorporated into the fullCallingPipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5151 348d0f76-0448-11de-a6fe-93d51630548a
to align to a reference other than what's specified in the header.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5133 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
Doing it manually for the moment so that there's at least something testing
this capability; will followup eventually with Mark to see whether we can
shape the VCF index generation code in such a way that it supports BAM index
testing as well.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5093 348d0f76-0448-11de-a6fe-93d51630548a
Moved VariantEval validation from FCPTest to PipelineTest.
Cleaned up some duplicate code for writing temp files during tests.
Moved FCPTest to playground namespace to match move for FCP.q.
Added a basic HelloWorldPipelineTest for the HelloWorld QScript.
Moved duplicated error handling from JobRunners into the FunctionEdge.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5068 348d0f76-0448-11de-a6fe-93d51630548a
pileup, resulting a two map() calls for the same locus (and no map call for
the locus immediately following).
Fixed bug and added comprehensive unit tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5067 348d0f76-0448-11de-a6fe-93d51630548a
very hard to validate and still very hard to use (requires core hacking to
support additional tags).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5038 348d0f76-0448-11de-a6fe-93d51630548a
- Reading the refseq table from the YAML if not specified on the command line.
- Removed obsolete -bigMemQueue now that CombineVariants runs in 4g.
- Added a -mountDir /broad/software option to work around adpr automount issues.
- Merged the LSF preexec used for automount into the shell script used to execute tasks.
- Using the LSF C Library to determine when jobs are complete instead of postexec.
- Updated queue.sh to match the changes above.
- Updated the FCPTest to match the changes above.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5036 348d0f76-0448-11de-a6fe-93d51630548a
test typo, which Khalid already fixed for me. Sorry, Khalid!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5035 348d0f76-0448-11de-a6fe-93d51630548a
Rather than try to fork the integration test process to get a pipe source
and sink, creates a new named pipe by Runtime.exec()ing the 'mkfifo' shell
command. We'll see whether this proves to be a reliable method for testing
streaming.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5028 348d0f76-0448-11de-a6fe-93d51630548a
a member field of RMDTrackBuilder was getting rebuilt every time it was
called, creating concurrency issues.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5001 348d0f76-0448-11de-a6fe-93d51630548a
primitive types were properly validated and throw the proper
MissingArgumentValue UserException. Before this fix, the error reported
was the infamous DePristo BSOD (Could not create module String because
an exception of type NullPointerException occurred caused by exception null).
Thanks Mauricio!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4980 348d0f76-0448-11de-a6fe-93d51630548a
hanna
kiran
kshakir
ebanks
asivache
depristo
rpoplin
aaron