Disabled the MFCP while the FCP gets an update.
Minor updates to email messages for upcoming scala 2.9.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5588 348d0f76-0448-11de-a6fe-93d51630548a
Fixed escaping expressions that have more than one space between arguments.
Updated example to match the wiki.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5516 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.
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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.
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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
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
- basic unit tests for interval sorting and merging with mix of mapped/unmapped.
- validation to ensure that locus walkers (really all non-read walkers) blow up with a user error when -L unmapped is specified.
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BAQ has generally useful improvements. Refactor code to make it easier for BAQUnitTest to run. minBaseQuality enforced on output, as well as input now. Added BAQUnitTest that checks that the BAQ calculation is performing as expected. Still needs to be expanded significantly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4804 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
Initial test to see how Bamboo will respond. More detailed email to follow.
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Unrelated change: in the sorted-target mode (when we read sorted target intervals one by on from a file), one can now specify multiple semicolon-separated interval files (all must be sorted). Not hugely useful probably, but makes --targetIntervals always process its values in exactly the same way, so we are consistent (it has been already taking ;-separated args in unsorted mode)
NwayIntervalMergingIterator: reads in multiple sorted GenomeLoc input streams (iterators) and presents them as a single sorted and merged stream
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argument. Brought it back, and added an integrationtest to make sure it
stays around.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4390 348d0f76-0448-11de-a6fe-93d51630548a
pieces of core that depend on playground. Most of these have been eliminated by
(temporarily) promoting Aaron's report system to core in this checkin. I'll
follow up with other changes in separately.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4350 348d0f76-0448-11de-a6fe-93d51630548a
*** Three integration tests had to change: ***
RecalibarationWalkersIntegrationTest:
One of the tests was using the interval as the snp track, and wasn't supplying a DbSNP track (for CountCovariates)
SequenomValidationConverterIntegrationTest:
relies on Plink ROD which we've removed.
PileupWalkerIntegrationTest:
we no longer have implicit interval tracks, so there isn't a rod name over the specified region. Otherwise the same result.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4292 348d0f76-0448-11de-a6fe-93d51630548a
in the reference. Reset routine is not accessible to any class outside
GenomeLocParser's package.
We'll have to do something more intelligent with this when the GATK goes
distributed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4275 348d0f76-0448-11de-a6fe-93d51630548a
kshakir
ebanks
depristo
hanna
aaron
bthomas
asivache