Story:
=====
- https://www.pivotaltracker.com/story/show/83259038
Changes:
=======
- Done minimal changes to make the fix after an arduous attempt to understand
CombineGVCFs code.
Test:
====
- Added a integration test to explicitly test for the bug.
- Updated a md5 changes as the bug was actually affecting one of the existing
integration tests.
Story:
-----
- https://www.pivotaltracker.com/story/show/83800586
Changes:
-------
- In GVCFWriter GQ is now recalculated out of the fianl PL array for the block.
Testing:
-------
- Updated affected integration test md5s
Add more logging to annotators, change loggers from info to warn
Add comments to testStrandBiasBySample()
Clarify comments in testStrandBiasBySample
remove logic for not prcossing an indel if strand bias (SB) was not computed
remove per variant warnings in annotate()
Log warnings if using the wrong annotator or missing a pedgree file
Log test failures once in annotate(), because HaplotypeCaller does not call initialize(). Avoid using exceptions
Fix so only log once in annotate(), Hardey-Weinberg does not require pedigree files, fix test MD5s so pass
Check if founderIds == null
Update MD5s from HaplotypeCaller integrations tests and clean up code
Change logic so SnpEff does not throw excpetions, change engine to utils in imports
Update test MD5s, return immediately if cannot annotate in SnpEff.initialization()
Post peer review, add more logging warnings
Update MD5 for testHaplotypeCallerMultiSampleComplex1, return null if PossibleDeNovo.annotate() is not called by VariantAnnotator
Story:
-----
https://www.pivotaltracker.com/story/show/80684230
Changes:
-------
- Corrected the bug: AlignmentUtils#createReadAlignedToRef was
not realigning against the reference but the best haplotype for
the read.
Test:
----
- Added integration test in HaplotypeCallerIntegrationTest to check
that the bug has been fixed.
- Fixed md5s modified by this change; these are cause due to small
changes in the state of the random-number generator and read vs
variant site overlapping.
CombineGVCFs now outputs ref conf for the duration of deletions so that SNPs occuring in other samples aligned with those deletions will be genotyped correctly
Reading the multiple GATKText files as a single stream, especially with new top level target executable jar files pointing to a lib folder.
Don't dirty the build with a new GATKText.properties if input files are unmodified.
Stop warning on undocumented abstract classes.
Fixed ClassNotFoundException/NoClassDefFoundError by fixing ResourceBundleExtractorDoclet artifact.
Excluding Exceptions from documentation.
Removed custom log4j dependency from ResourceBundleExtractorDoclet.
Stop generating the dependency reduced pom during shade.
Stop regenerating gsalib when the files are already up to date.
Disabled mvn site generation from external-example.
Moved top level target symlinks to package jar files to under target/package.
Executable jar files are placed under target/executable with the new target[/lib] directories.
Under top level target, symlinks to *either* the package *or* the executable jars replace what was a symlink to the package jar path.
Allow disabling of the shade package.
ant-bridge.sh by default only builds executable jars, and doesn't package by default, as did the old ant build.xml.
Added a new package_path.sh utility script for other scripts to use instead of anything in the target folder.
rpoplin
Valentin Ruano-Rubio
Geraldine Van der Auwera
Phillip Dexheimer
Ron Levine
Alec Wysoker
droazen
Menachem Fromer
ldgauthier
jmthibault79
kshakir
Khalid Shakir