In these cases, where the alignment contains multiple indels, we output a single complex
variant instead of the multiple partial indels.
We also re-enable dangling tail recovery by default.
-- AD,DP will now correspond directly to the reads that were used to construct the PLs
-- RankSumTests, etc. will use the bases from the realigned reads instead of the original alignments
-- There is now no additional runtime cost to realign the reads when using bamout or GVCF mode
-- bamout mode no longer sets the mapping quality to zero for uninformative reads, instead the read will not be given an HC tag
-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
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.
GATK classes accessing package protected htsjdk classes changed to new package names.
POMs updated to support merging of sam/tribble/variant -> htsjdk and changes to picard artifact.
RodSystemValidation outputs changed due to variant codec packages changes, requiring test md5 updates.
Second of four commits for picard/htsjdk package rename.
GATK classes accessing package protected htsjdk classes will need new package names.
POMs will merge sam/tribble/variant into htsjdk.
Move only, contents updated in next commit.
First of four commits for picard/htsjdk package rename.
The JNI treats shared memory as critical memory and doesn't allow any
parallel reads or writes to it until the native code finishes. This is
not a problem *per se* it is the right thing to do, but we need to
enable **-nct** when running the haplotype caller and with it have
multiple native PairHMM running for each map call.
Move to a copy based memory sharing where the JNI simply copies the
memory over to C++ and then has no blocked critical memory when running,
allowing -nct to work.
This version is slightly (almost unnoticeably) slower with -nct 1, but
scales better with -nct 2-4 (we haven't tested anything beyond that
because we know the GATK falls apart with higher levels of parallelism
* Make VECTOR_LOGLESS_CACHING the default implementation for PairHMM.
* Changed version number in pom.xml under public/VectorPairHMM
* VectorPairHMM can now be compiled using gcc 4.8.x
* Modified define-* to get rid of gcc warnings for extra tokens after #undefs
* Added a Linux kernel version check for AVX - gcc's __builtin_cpu_supports function does not check whether the kernel supports AVX or not.
* Updated PairHMM profiling code to update and print numbers only in single-thread mode
* Edited README.md, pom.xml and Makefile for users to pass path to gcc 4.8.x if necessary
* Moved all cpuid inline assembly to single function Changed info message to clog from cinfo
* Modified version in pom.xml in VectorPairHMM from 3.1 to 3.2
* Deleted some unnecessary code
* Modified C++ sandbox to print per interval timing
Story:
https://www.pivotaltracker.com/story/show/68220438
Changes:
- PL-less input genotypes are now uncalled and so non-variant sites when combining GVCFs.
- HC GVCF/BP_RESOLUTION Mode now outputs non-variant sites in sites covered by deletions.
- Fixed existing tests
Test:
- HaplotypeCallerGVCFIntegrationTest
- ReferenceConfidenceModelUnitTest
- CombineGVCFsIntegrationTest
* This addresses PT Bug 69741902
* Added a required IMR argument to FilePointer, BAMScheduler, IntervalSharder, and SAMDataSource
* This rule is used by FilePointer.combine and FilePointer.union
* Added unit and integration tests
kshakir
Khalid Shakir
David Roazen
Eric Banks
Ryan Poplin
Phillip Dexheimer
Nigel Delaney
Nigel Delaney
Chris Whelan
Menachem Fromer
Valentin Ruano Rubio
Karthik Gururaj
jmthibault79
Laura Gauthier
Phillip Dexheimer