-When parental genotypes are available, implements an HMM on genotype observations in the quartet.
-Outputs IBD regions as well as per-site posterior probabilities of being in each IBD state.
-Includes an experimental heuristic based mode for when parental genotypes are not available.
-Made a method in MendelianViolation public static to reuse code.
-Added the mockito library to private/gatk-tools-private/pom.xml
- Fields in the header are delimited with the pipe character
- Header is now split into two lines to improve spacing
- Field width in header and progress lines auto-adjusts to length of "processing units" label (sites, active regions, etc)
- Addresses PT 69725930
-They are now only computed when necessary
-Log10Cache is dynamically resizable, either by calling get() on an out-of-range value or by calling ensureCacheContains
-Log10FactorialCache and JacobianLogTable are initialized to a fixed size on first access and are not resizable
-Addresses PT 69124396
-Make BaseTest.createTempFile() mark any possible corresponding index files for deletion on exit
-Make WalkerTest mark shadow BCF files and auxiliary for deletion on exit
-Make VariantRecalibrationWalkersIntegrationTest mark PDF files for deletion on exit
-- disabling HC+VA integration test because, as noted in the comments, it keeps switching PairHMM implementations and giving different results at a particular site used in that particular test
Stories:
- https://www.pivotaltracker.com/story/show/69577868
Changes:
- Added a epsilon difference tolerance in weight comparisons.
Tests:
- Added HaplotypeCallerIntegrationTest#testDifferentIndelLocationsDueToSWExactDoubleComparisonsFix
- Updated md5 due to minor likelihood changes.
- Disabled a test for PathUtils.calculateCigar since does not work and is unclear what is causing the error (needs original author input)
To reduce merge conflicts, this commit modifies contents of files, while file renamings are in previous commit.
See previous commit message for list of changes.
To reduce merge conflicts, this commit only renames files, while file modifications are in next commit.
Some updates/fixes here are actually included in the next commit.
= Maven updates
Moved artifacts to new package names:
* private/queue-private -> private/gatk-queue-private
* private/gatk-private -> private/gatk-tools-private
* public/gatk-package -> protected/gatk-package-distribution
* public/queue-package -> protected/gatk-queue-package-distribution
* protected/gatk-protected -> protected/gatk-tools-protected
* public/queue-framework -> public/gatk-queue
* public/gatk-framework -> public/gatk-tools-public
New poms for new artifacts and packages:
* private/gatk-package-internal
* private/gatk-queue-package-internal
* private/gatk-queue-extensions-internal
* protected/gatk-queue-extensions-distribution
* public/gatk-engine
Updated references to StingText.properties to GATKText.properties.
Updated ant-bridge.sh to use gatk.* properties instead of sting.*.
= Engine updates
Renaming files containing engine parts from o.b.gatk.tools to o.b.gatk.engine.
Changed package references from tools to engine for CommandLineGATK, GenomeAnalysisEngine, ReadMetrics, ReadProperties, and WalkerManager.
Changed package reference tools.phonehome to engine.phonehome.
Renamed classes *Sting* to *GATK*, such as ReviewedGATKException.
= Test updates
Moved gatk example resources.
Moved test engine files from tools to engine packages.
Moved resources for phonehome to proper package.
Moved test classes under o.b.gatk into packages:
* o.b.g.utils.{BaseTest,ExampleToCopyUnitTest,GATKTextReporter,MD5DB,MD5Mismatch,TestNGTestTransformer}
* o.b.g.engine.walkers.WalkerTest
Updated package names in DependencyAnalyzerOutputLoaderUnitTest's data.
= Queue updates
Moving queue scripts to location where generated extensions can be used.
Renamed *.q to *.scala, updating licenses previously missed by git hooks.
Moved queue extensions to new artifact gatk-queue-extensions.
Fixed import statments frequently merge-conflicting on FullProcessingPipeline.scala.
= BWA
Added README on how to obtain and include bwa as a library.
Updated libbwa build.
Fixed packaged names under bwa/java implementation.
Updated contents of BWCAligner native implementation.
= Other fixes
Don't duplicate the resource bundle entries by both unpacking *and* appending.
(partial fix) Staged engine and utils poms to build GATKText.properties, once Utils random generator dependency on GATK engine is fixed.
Re-enabled custom testng listeners/reporters and moved testng dependencies to the gatk-root.
Updated comments referencing Sting with GATK.
Moved a couple untangled classes from gatk-tools-public to gatk-utils and gatk-engine.
Chris Whelan
Ryan Poplin
droazen
Khalid Shakir
Eric Banks
Menachem Fromer
jmthibault79
Phillip Dexheimer
Valentin Ruano Rubio
EvolvedMicrobe
Nigel Delaney
kshakir
Karthik Gururaj
Laura Gauthier