-Added targets to run unit and integration tests on the fully-packaged GATK jar,
and pipeline tests on the fully-packaged Queue jar. Once enabled in Bamboo,
these will provide greatly-enhanced protection against breakage in the binary
release.
-Unconditionally include all of the subset of org.broadinstitute.sting
included in the intermediate jars GenomeAnalysisTK.jar, StingUtils.jar,
etc. in the final, fully-packaged jar. This:
* is necessary to get tests to run on the fully-packaged jar
* decreases the chances of a class that is a runtime-only
dependency getting left out of the binary release
* only slightly increases the size of the binary release
(before: 9352465 bytes, after: 10985482 bytes)
The public integration test VariantContextIntegrationTest was dependent on the
private walker TestVariantContextWalker. Moved this walker to public/java/test
(NOT public/java/src, since this walker is only used by the test suite) to avoid
errors during public-only tests.
-- MD5 db had spelling error; fixed
-- Bug in AlignmentUtils resulted in some bases not being color space corrected. The integration test caught the change, and it's clear that the new version is correct, as the prev. version was not considering the last the N qualities for reads with a ND operation.
-- SimpleTimer is now threadsafe using synchronized method keywords
-- Bug fix for alignmentToByteArray() where the N case was refPos++ not the now correct refPos += elementLength
Having SnpEff grouped with the Experimental annotations was proving problematic, since it
requires a rod. Placing it in its own group should improve the situation somewhat, making it
easier to request "all annotations except for SnpEff".
This allows the annotation classes to perform any necessary initialization/validation.
For example, it allows the SnpEff annotator to (among other things) validate its rod binding.
This will prevent a NullPointerException when SnpEff annotation is requested but no rod binding
is present.
Added an integration test to cover this case so that it doesn't break again.
-- Changes associated code throughout the codebase
-- Updated necessary (but minimal) UnitTests to reflect new behavior
-- Much better makealleles() function in VC.java that enforces a lot of key constraints in VC
-- For no apparent reason we were using a HashSet to store the ReadFilters, so the order of operations was really arbitrarily applied. The order now is
(1) the order of the walker intrinsic filters
(2) read group black list (if provided)
(3) command line filters (if provided)
classloading of bcel*.jar/ant-apache-bcel*.jar. Switching instead to manually
specifying a minimal set of packages/classes to include in the vcf.jar via
build.xml, and adding a unit test which creates a limited classloader
only aware of vcf.jar and tribble.jar and tries to use it to load the core
classes in the vcf jar.
Hopefully third time's the charm.
-- The GATK will now throw a user exception if it opens a SAM/BAM file that doesn't have at least one RG defined
-- LIBS again throws an error if the complete list of samples isn't provided
-- Updating ExmpleCountLociPipeline test to use the well-formated versions of the exampleBAM and exampleFASTA files in testdata, instead of the old broken ones in validation_data.
-- Convenience constructors for UserExceptions.MalformedBAM
David Roazen
Mark DePristo
Eric Banks
Mauricio Carneiro
Guillermo del Angel
Matt Hanna
Khalid Shakir