Renamed M2 to MuTect2
Renamed ContaminationWalker to ContEst
Refactored related tests and usages (including in Queue scripts)
Moved M2 and ContEst + accompanying classes from private to protected
Made QSS a StandardSomaticAnnotation (new annotation group/interface) to prevent it from being sucked in with the rest of the StandardAnnotation group
ReadAdaptorTrimmer (unsound and untested)
BaseCoverageDistribution (redundant with DiagnoseTargets)
CoveredByNSamplesSites (redundant with DiagnoseTargets)
FindCoveredIntervals (redundant with DiagnoseTargets)
VariantValidationAssessor (has a scary TODO -- REWRITE THIS TO WORK WITH VARIANT CONTEXT comment and zero tests)
LiftOverVariants, FilterLiftedVariants and liftOverVCF.pl (in #1106) (use Picard liftover tool)
sortByRef.pl (use Picard SortVCF)
ListAnnotations (useless)
Also deleted the java archive from the private repository (old junk we never use)
Grouped default output annotations to keep them from getting dropped when -A is specified; addresses #918
Also refactored code shared by ExcessHet and InbreedingCoeff
CRAM now requires .bai index, just like BAM.
Test updates:
- Updated existing MD5s, as TLEN has changed.
- Tests multiple contigs.
- Tests several intervals per contig.
- Tests when `.cram.bai` is missing, even when `.cram.crai` is present.
Updated gatk docs for CRAM support, including:
- Arguments that work for both BAM and CRAM listed as such.
- Arguments that don't work for CRAM either explicitly say "BAM" or "doesn't work for CRAM".
- Instructions on how to recreate a `.cram.bai` using cramtools.
Cleaned up IntelliJ IDEA warnings regarding `Arrays.asList()` -> `Collections.singletonList()`.
When using CatVariants, VCF files were being sorted solely on the base
pair position of the first record, ignoring the chromosome. This can
become problematic when merging files from different chromosomes,
espeically if you have multiple VCFs per chromosome.
As an example, assume the following 3 lines are all in separate files:
1 10
1 100
2 20
The merged VCF from CatVariants (without -assumeSorted) would read:
1 10
2 20
1 100
This has the potential to break tools that expect chromosomes to be
contiguous within a VCF file.
This commit changes the comparator from one of Pair<Integer, File> to
one of Pair<VariantContext, File>. We construct a
VariantContextComparator from the provided reference, which will sort
the first record by chromosome and position properly. Additionally, if
-assumeSorted is given, we simply use a null VariantContext as the first
record, which will all be equal (as all will be null)
-We now pull htsjdk and picard from maven central.
-Updated the GATK codebase as necessary to adapt to changes in the Feature
interface.
-Since VCFHeader now requires that all header lines have unique keys, uniquified
the keys of GVCFBlock header lines by including the min/max GQ in the key.
Updated MD5s accordingly.
-Other MD5s changed as a result of an htsjdk fix to eliminate "-0" in VCF output.
Exclude MQ0BySample
Move SD and TRA to new StandardUGAnnotation interface
There is now annotation interface (StandardUGAnnotation) holding annots that are standard in UG but should't be used as they are now with HC. This allows us to not have to exclude these annotations explicitly in HC, but still be able to use them for development purposes.
Fairly minor if plentiful fixes to various gatkdocs. Merging this without formal review since all tests pass, the gatkdocs build, and no one really wants to review corrections to grammar, typos and layout for 120+ documents. Review will be done by users in production ;-)
Build a ReferenceContext in ActiveRegionWalkers to pass in to annotation engine so we can call the TandemRepeatAnnotator from M2
Make TandemRepeatAnnotator default annotation for M2.
Setup (but don't use yet) HC-style contamination downsampling.
New HC integration test with TandemRepeatAnnotator
- ASEReadCounter (public tool) replce Tuuli's script to produce the input to Manny's tool.
It count the number of reads that support the ref allele and the alt allele, filtereing low qual reads and bases and keep only properPaired reads
- ASECaller (private tool) take both RNA and DNA, and produce ontingencyTables ** still under development **
minor changes in other tools:
- update RNA HC variant calling scala script
- expose FS method pValueForContingencyTable to be able to call it from ASEcaller
In ASEReadCounter:
- allow different option to deal with overlaping read from the same fragment
- add option to ignore or include indels in the pileups
- add option to disabled DuplicateRead
add ASEReadCounterIntegrationTest.java and files for the test
* Removed unused annotations (CCC and HWP)
* Renamed one of the two GC annotations to "IGC" (for Interval GC)
* Revved picard & htsjdk (GATK constants are now removed from htsjdk)
* PT 82046038
Add multi-allele test for info field annotations
Fix to process all types of INFO annotations
roll back to previous version, removes INFO and FORMAT
Correct @return for VariantAnnotatorEngine.getNonReferenceAlleles()
Enhance comments and clean up multi-allelic logic, handle header info number = R
only parse counts of A & R
Add INFO for AC
update MD5
Performance enhancement, only parse multiallelic with a count A or R
Make argument final in getNonReferenceAlleles()
Code cleanup, add exceptions for bad expression/allele size mismatch and missing header info for an expression
Change exception to warning for expression value/number of alleles check
remove adevertised exceptions
* PT 84242218
* Note that FORMAT fields behave the same as INFO fields - if the annotation has a count of A (one entry per Alt Allele), it is split across the multiple output lines. Otherwise, the entire list is output with each field
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
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.
Fixed off by one error in size calculation IntervalUtils.scatterContigIntervals().
In test for fewer files than intervals, adjusted expected intervals.
In test for more files than intervals, adjusted expected exception.
ldgauthier
Geraldine Van der Auwera
seru71
Ron Levine
meganshand
Yossi Farjoun
Takuto Sato
Kate Noblett
Ami Levy Moonshine
Bertrand Haas
Khalid Shakir
David Benjamin
Louis Bergelson
Joseph White
Eric Banks
John Wallace
David Roazen
Ami Levy-Moonshine
Phillip Dexheimer
rpoplin
Ron Levine
Chris Smowton
Sheila Chandran