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.
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rather than a UserException when an the input argument is specified without
an argument value.
The magnitude of code required to fix this points to a need to give the
command-line argument system a good spring cleaning.
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Updated the package of ValidationGenotyper to match the file location.
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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.
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of a sequence dictionary and related info. This will hopefully eliminate the cases in
which the refseq track depends a sequence dictionary / contig parser that hasn't been
specified.
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- Number of insertions
- Number of deletions
- Length distribution for indels.
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Added a @Hidden experimental argument -validate to VariantEval that allows external JEXL assertions that must evaluate to true will throw an exception.
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dependent on the contents of the integrationtest directory. Will figure
out how to better manage the integrationtest directory at some point in
the future.
- Up the max heap size for tests.
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- Add StingTextReporter, which provides a text dump of the errors to the
console. Had to create our own reporter (inheriting from the standard
TestNG TextReporter) to work around a configuration issue with the
TextReporter. In an ideal world, I'd report this on the TestNG mailing
list and help them resolve the issue, but this solution is relatively
robust at the moment and life is too short.
- Added back the failed test listener, which generates the testng-failed.xml
file.
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- Changed RMDTrackBuilder to use SequenceDictionaryUtils.validateDictionaries for ref <-> ROD sequence dictionary validation.
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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.
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depristo
ebanks
delangel
aaron
hanna
kshakir
bthomas
fromer
rpoplin