(Right now it only works if all members of the trio are called.)
Takes posteriors as input, defaulting to PLs
Added annotations for possible de novos for us in full genotype refinement pipeline
Added family priors to CGP integration test.
Changed CGP to use PP tag instead of GP tag because posteriors are Phred-scaled. Updated CGP integration test md5s to reflect change.
- New arguments are nda, hets, indelHeterozygosity, stand_call_conf, stand_emit_conf, ploidy, and maxAltAlleles
- Addresses PT 70110918
- To do this, moved those arguments out of the StandardCallerArgumentCollection into a new GenotypeCalculationArgumentCollection, which is now included as a member of SCAC
-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.
Eric Banks
Laura Gauthier
Phillip Dexheimer
Valentin Ruano Rubio
EvolvedMicrobe
Nigel Delaney
David Roazen
Ryan Poplin
Khalid Shakir
Karthik Gururaj