1) There is now a different parameter for sample name (-sn), sample file (-sf) or sample expression (-se). The unexpected behavior of the previous implementation was way too tricky to leave unchecked. (if you had a file or directory named after a sample name, SV wouldn't work)
1b) Fixed a TODO added by Eric -- now the output vcf always has the samples sorted alphabetically regardless of input (this came as a byproduct of the implementation of 1)
2) Discordance and Concordance now work in combination with all other parameters.
3) Discordance now follows Guillermo's suggestion where the discordance track is your VCF and the variant track is the one you are comparing to. I have updated the example in the wiki to reflect this change in interpretation.
4) If you DON'T provide any samples (-sn, -se or -sf), SelectVariants works with all samples from the VCF and ignores sample/genotype information when doing concordance or discordance. That is, it will report every "missing line" or "concordant line" in the two vcfs, regardless of sample or genotype information.
5) When samples are provided (-sn, -se or -sf) discordance and concordance will go down to the genotypes to determine whether or not you have a discordance/concordance event. In this case, a concordance happens only when the two VCFs display the same sample/genotype information for that locus, and discordance happens when the disc track is missing the line or has a different genotype information for that sample.
6) When dealing with multiple samples, concordance only happens if ALL your samples agree, and discordance happens if AT LEAST ONE of your samples disagree.
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Integration tests:
1) Discordance and concordance test added
2) All other tests updated to comply with the new 'sorted output' format and different inputs for samples.
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Methods for handling sample expressions and files with list of samples were added to SampleUtils. I recommend *NOT USING* the old getSamplesFromCommandLineInput as this mixing of sample names with expressions and files creates a rogue error that can be challenging to catch.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6072 348d0f76-0448-11de-a6fe-93d51630548a
Bug smashes for the MCFP:
Synchronized access to LSF library and modifications to the QGraph.
If values are missing from the graph with -run make sure to exit with a non-zero.
Refactored QGraph to pre-generate a unique Int for each QNode speeding up getHashCode/equals inside the graph.
Added jobPriority and removed jobLimitSeconds from QFunction.
All scatter gather is by default in a single sub directory queueScatterGather.
Moved some FCPTest into BaseTest/PipelineTest for use by MFCPTest.
Rev'ed the 1000G bams used for validation from v1 to v2 and added code to look for the bams before running other tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5247 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
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
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
When a QGraph is empty displaying a warning instead of crashing with an JGraph internal assertion error.
Cleaned up code using the Log4J root logger and explicitly talking to a logger for Sting.
When integration tests are run detecting that the logger has already been setup so that messages aren't logged twice.
Updated from Ivy 2.2.0-rc1 to 2.2.0.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4707 348d0f76-0448-11de-a6fe-93d51630548a
Initial test to see how Bamboo will respond. More detailed email to follow.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4609 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
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