remove final keyword before refMap and altMap, constructHaplotype() changes their values
return ArtificialHaplotype from constructHaplotype instaed of passing as an argument
Add logic so arraycopy does not throw an IndexOutOfBoundsException, add test for a long insert
remove TODO comment after activeProbThreshold
recover static ACTIVE_PROB_THRESHOLD for unit tests
Add min/max values for active_probability_threshold parameter
Move activeProbThreshold parameter to GATKArguemtnCollection
define ACTIVE_PROB_THRESHOLD in unit tests
add construction of argCollection in in ctor
Move arguments from GATKArgumentCollection to ActiveRegionWalker
Throw exception if threshold < 0 or > 1 in ActivityProfile ctor
max propogation distance parameter to ActiveRegionWalker for AcrtivityProfile
Use polymorphic getMaxProbPropagationDistance() so BandPassActivityProfile computes the crrect region size cutoff
Get the maxProbPropagationDistance from the super class's method, instead of directly, this is safer
Removed extraneous command line imports and make maxProbPropagationDistance a hidden argument
remove limit check for activeProbThreshold, not necessary because the check is made when imput as a command line arg
Remove extra 'region' in the doxygen param description for maxProbPropagationDistance
* This argument forces GATK to always write every record in the VCF format field, even if some records at the end are missing and could be removed
* Revved htsjdk and picard
* PT 70993484
Changes:
-------
* Updated current unit and integration test to use the new API components.
* Added unit tests for new classes AFPriorProvider and AFCalculatorProviders.
* Added integration test for mixed ploidy GenotypeGVCFs and CombineGVCFs
Changes:
-------
* GenotypingEngine uses now a AFCalc provider instead of
its own thread-local with one-time initialized and fixed
AF calculator.
* All walkers that use a GenotypingEngine now are passing
the appropiate AF calculator provider. For now most
just use a fix calculator (FixedAFCalculatorProvider)
except GenotypeGVCFs as this one now can cope with
mixture of ploidies failing-over to a general-ploidy
calculator when the preferred implementation is not
capable to handle a site's analysis.
* Arguments involved are --no_cmdline_in_header, --sites_only, and --bcf for VCF files and --bam_compression, --simplifyBAM, --disable_bam_indexing, and --generate_md5 for BAM files
* PT 52740563
* Removed ReadUtils.createSAMFileWriterWithCompression(), replaced with ReadUtils.createSAMFileWriter(), which applies all appropriate engine-level arguments
* Replaced hard-coded field names in ArgumentDefinitionField (Queue extension generator) with a Reflections-based lookup that will fail noisily during extension generation if there's an error
Explicitly including gatk/queue test-jar artifacts in package test classpaths.
SelectVariantsIntegrationTest#testInvalidJexl now resets the JexlEngine silent flag that VariantFiltration.initialize() toggles.
External example no longer tries to unpack nonexistent gatk artifact jars during package tests.
Same changes fixed the problem for GenotypeGVCFs and CombineGVCFs.
Stories:
- https://www.pivotaltracker.com/story/show/77626044
- https://www.pivotaltracker.com/story/show/77626854
Changes:
- Generalized the code for the merging in GATKVariantContextUtils to cope
with ploidy != 2.
- GenotypeGVCFs now check that the input's ploidy conform to the '-ploidy'
argument.
- Moved out Refernce Confidence VC merging code from GATKVariantContextUtils
so that we can keep new code in protected.
Caveats:
- GenotypeGVCFs only can deal with input files that have the same ploidy in
all positions; the one that the user MUST indicate in the -ploidy argument
(if different to the default 2).
- CombineGVCFs won't necessarely complain if its passed mixed ploidy
inputs but you won't be able to genotype it with GenotypeGVCFs.
Test:
- Removed deprecated unit tests for GATKVariantContextUtils.
- Moved unit-tests regarding GVCF merging from GATKVariantContextUtilsUnitTest
to ReferenceConfidenceVariantContextUtilsUnitTest.
- Added unit test for new code for mapping genotype indices between allele
index encoding in GenotypeLikelihoodCalculator.
- GenotypeGVCFs and CombineGVCFs original integration test are unaffected
by the change.
- Added tetraploid run integration tests to check on non-diploid execution
of GenotypeGVCFs and CombineGVCFs.
Changed tests and scripts to use gatkdir full path instead of relative testdata/qscripts symbolic links.
Although symlinks not created, left the symlink deletion script execution with a comment about future removal.
Re-enabled example UG pipeline queue test.
Replaced all hardcoded strings of {public,private}/testdata with BaseTest variables.
Refactored temp list creation method from ListFileUtilsUnitTest to BaseTest.createTempListFile.
Removed list files with hardcoded paths, now using createTempListFile instead with private test dir variable.
Story:
https://www.pivotaltracker.com/story/show/77250524
Changes:
- Remove the annotating code in GeneralPloidyExactAFCalc (GPEAFC) class.
- Added the asAlleleList to GenotypeAlleleCounts class and get (GPEAFC) to use that instead of implementing its own (nicer and more reusable code).
- Removed the explicit addition of AlleleCountBySample fields to the VCF header by the walker initialize
- Added utility methods in Utils to wrap and int[] array into a List<Integer>, and double[] array into a List<Double> efficiently.
Test:
- Added unit-testing for asAlleleList in GenotypeAlleleCountsUnitTest (within testFirst and testNext).
- Added unit-testing for new methods in Utils : asList(int[]) and asList(double[])
- Changed UG General Ploidy test to add explicitly those annotations.
- Non-trivial changes in integration tests involving non-diploid runs (namelly haploid and tetraploid) as they are not showing
those annotations anylonger, so the MD5s have been changed accordingly.
Changes in several walker to use new sample, allele closed lists and new GenotypingEngine constructors signatures
Rebase adoption of new calculation system in walkers
If any pair of variants occurs on all used haplotypes together, then we propagate that information into the gVCF.
Can be enabled with the --tryPhysicalPhasing argument.
- Read groups that are excluded by sample_name, platform, or read_group arguments no longer appear in the header
- The performance penalty associated with filtering by read group has been essentially eliminated
- Partial fulfillment of PT 73075482
Stories:
https://www.pivotaltracker.com/story/show/70222086https://www.pivotaltracker.com/story/show/67961652
Changes:
Done some changes that I missed in relation with making sure that all PairHMM implentations use the same interface; as a consequence we were running always the standard PairHMM.
Fixed some additional bugs detected when running it on full wgs single sample and exom multi sample data set.
Updated some integration test md5s.
Fixing GraphBased bugs with new master code
Fixed ReadLikelihoods.changeReads difficult to spot bug.
Changed PairHMM interface to fix a bug
Fixed missing changes for various PairHMM implementations to get them to use the new structure.
Fixed various bugs only detectable when running with full sample(s).
Believe to have fixed the lack of annotations in UG runs
Fixed integrationt test MD5s
Updating some md5s
Fixed yet another md5 probably left out by mistake
The array structure should be faster to populate and query (no properly benchmarked) and reduce memory footprint considerably.
Nevertheless removing PairHMM factor (using likelihoodEngine Random) it only achieves a speed up of 15% in some example WGS dataset
i.e. there are other bigger bottle necks in the system. Bamboo tests also seem to run significantly faster with this change.
Stories:
https://www.pivotaltracker.com/story/show/70222086https://www.pivotaltracker.com/story/show/67961652
Changes:
- ReadLikelihoods added to substitute Map<String,PerSampleReadLikelihoods>
- Operation that involve changes in full sets of ReadLikelihoods have been moved into that class.
- Simplified a bit the code that handles the downsampling of reads based on contamination
Caveats:
- Still we keep Map<String,PerReadAlleleLikelihoodsMap> around to pass to annotators..., didn't feel like change the interface of so many public classes in this pull-request.
In particular, it was possible to specify arguments for Files or Compound types without values
Added a special "none" value for annotations, since a bare "-A" is no longer allowed
Delivers PT 71792842 and 59360374
ValidationStringency was moved from htsjdk.samtools.SAMFileReader to htsjdk.samtools
samtools find BAM index file method was also moved (and made public!)
- Edited intervals merging docs for correctness & clarity
- Edited VQSR arg docs and made mode required (+added -mode SNP to VQSR tests)
- Moved PaperGenotyper to Toy Walkers to declutter the actually useful docs
- Moved GenotypeGVCFs to Variant Discovery category and clarified a few points
- Clarified that the -resource argument depends on using the -V:tag format
- Clarified how the pcr indel model works
- Added caveat for -U ALLOW_N_CIGAR_READS
- Added MathJax support for displaying equations in GATKDocs
- Updated HC example commands and caveats
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.
Sheila Chandran
rpoplin
Ron Levine
Phillip Dexheimer
Laura Gauthier
Geraldine Van der Auwera
Ron Levine
Valentin Ruano-Rubio
Khalid Shakir
droazen
Eric Banks
Michael Linderman
jmthibault79
kshakir
Nigel Delaney
Nigel Delaney
Chris Whelan
Menachem Fromer
Karthik Gururaj