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
Adding the first version of the techdev pipeline (tdPipeline)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4943 348d0f76-0448-11de-a6fe-93d51630548a
using one as though it was. Fixed, and debug code reverted.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4917 348d0f76-0448-11de-a6fe-93d51630548a
streaming/piping VCFs into the GATK. Notable changes:
- Public interface to RMDTrackBuilder is greatly simplified; users can use it only to build
RMDTracks and lookup codecs.
- RODDataSource and RMDTrack are no longer functionally at the same level; RODDataSources now
manage RMDTracks on behalf of the GATK, and the only direct consumers of the RMDTrack class
are the walkers that feel the need to access the ROD system directly. (We need to stamp out
this access pattern.
A few minor warts were introduced as part of this process, labeled with TODOs. These'll be
fixed as part of the VCF streaming project.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4915 348d0f76-0448-11de-a6fe-93d51630548a
into the CommandLine* classes. This makes it easier for external functionality
(such as the VCF streamer) to use GenomeAnalysisEngine directly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4897 348d0f76-0448-11de-a6fe-93d51630548a
unmapped reads and explicitly excluding (-XL unmapped) unmapped reads, augmenting
the suite of unit tests already put in place.
'-L unmapped' seems safe to use; go for it, but please validate results against
samtools flagstat when the process finishes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4849 348d0f76-0448-11de-a6fe-93d51630548a
depristo
hanna
ebanks
kshakir
rpoplin
aaron
carneiro