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
story:
https://www.pivotaltracker.com/story/show/69648104
description:
This read transformer will refactor cigar strings that contain N-D-N elements to one N element (with total length of the three refactored elements).
This is intended primarily for users of RNA-Seq data handling programs such as TopHat2.
Currently we consider that the internal N-D-N motif is illegal and we error out when we encounter it. By refactoring the cigar string of
those specific reads, users of TopHat and other tools can circumvent this problem without affecting the rest of their dataset.
edit: address review comments - change the tool's name and change the tool to be a readTransformer instead of read filter
Description:
Transforms a delegation dependency from HC to UG genotyping engine into a reusage by inhertance where HC and UG engines inherit from a common superclass GenotyperEngine
that implements the common parts. A side-effect some of the code is now more clear and redundant code has been removed.
Changes have a few consequence for the end user. HC has now a few more user arguments, those that control the functionality that HC was borrowing directly from UGE.
Added -ploidy argument although it is contraint to be 2 for now.
Added -out_mode EMIT_ALL_SITES|EMIT_VARIANTS_ONLY ...
Added -allSitePLs flag.
Stories:
https://www.pivotaltracker.com/story/show/68017394
Changes:
- Moved (HC's) GenotyperEngine to HaplotypeCallerGenotyperEngine (HCGE). Then created a engine superclass class GenotypingEngine (GE) that contains common parts between HCGE and the UG counterpart 'UnifiedGenotypingEngine' (UGE). Simplified the code and applied the template pattern to accomodate for small diferences in behaviour between both caller
engines. (There is still room for improvement though).
- Moved inner classes and enums to top-level components for various reasons including making them shorter and simpler names to refer to them.
- Create a HomoSpiens class for Human specific constants; even if they are good default for most users we need to clearly identify the human assumption across the code if we want to make
GATK work with any species in general; i.e. any reference to HomoSapiens, except as a default value for a user argument, should smell.
- Fixed a bug deep in the genotyping calculation we were taking on fixed values for snp and indel heterozygisity to be the default for Human ignoring user arguments.
- GenotypingLikehooldCalculationCModel.Model to Gen.*Like.*Calc.*Model.Name; not a definitive solution though as names are used often in conditionals that perhaps should be member methods of the
GenLikeCalc classes.
- Renamed LikelihoodCalculationEngine to ReadLikelihoodCalculationEngine to distinguish them clearly from Genotype likelihood calculation engines.
- Changed copy by explicity argument listing to a clone/reflexion solution for casting between genotypers argument collection classes.
- Created GenotypeGivenAllelesUtils to collect methods needed nearly exclusively by the GGA mode.
Tests :
- StandardCallerArgumentCollectionUnitTest (check copy by cloning/reflexion).
- All existing integration and unit tests for modified classes.
-Only works with single-sample vcfs
-As with bams, the user must provide a file mapping the absolute path to
each vcf whose samples are to be renamed to the new sample name for that
vcf. The argument is the same as for bams: --sample_rename_mapping_file,
and the mapping file may contain a mix of bam and vcf files should the
user wish.
-It's an error to attempt to remap the sample names of a multi-sample
or sites-only vcf
-Implemented at the codec level at the instant the vcf header is first
read in to minimize the chances of downstream code examining vcf
headers/records before renaming occurs.
-Integration tests are in sting, unit tests are in picard
-Rev picard et. al. to 1.111.1902
Following reviewers comments the command line interface has been simplified.
All extra strict validations are performed by default (as before) and the
user has to indicate which one he/she does not want to use with --validationTypeToExclude.
Before he/she was able to indicate the only ones to apply with --validationType but that has been scrapped out.
Stories:
- https://www.pivotaltracker.com/story/show/68725164
Changes:
- Removed validateType argument.
- Improved documentation.
- Added some warnning log message on suspicious argument combinations.
Tests:
- ValidateVariantsIntegrationTest#*
-- This results in much more consistent distribution of LOD scores for SNPs and Indels.
-- Removing genotype summary stats since they are now produced by default.
-- Added functionality to specify certain subsets of the training data to be used in Tranche file generation, -good:tranche=true set.vcf
More concretelly Picard's strict VCF validation does not like that there is alternative alleles that are not participating in any genotype call across samples.
This is an issue with GVCF in the single-sample pipeline where this is certainly expected with <NON_REF> and other relative unlikely alleles.
To solve this issue we allow the user to exclude some of the strict validations using a new argument --validationTypeToExclude. In order to avoid the validation
issue with GVCF the user needs to add the following to the command line: '--validationTypeToExclude ALLELES'
Story:
https://www.pivotaltracker.com/story/show/68725164
Changes:
- Added validateTypeToExclude argument to ValidateVariants walker.
- Implemented the selective exclusion of validation types.
- Added new info and improved existing documentation of the ValidateVariants walker.
Tests:
- ValidateVariantsIntegrationTest#testUnusedAlleleError
- ValidateVariantsIntegrationTest#testUnusedAlleleFix
In some cases, the program records were being removed from the BAM headers by the GATK engine
before we applied the check for reduced reads (so we did not fail appropriately). Pushed up the
check to happen before the PG tags are modified and added a unit test to ensure it stays that way.
It turns out that some UG tests still used reduced bams so I switched to use different ones.
Based on reviewer feedback, made it more generic so that it's easy to add new unsupported tools.
Previously it required you to create a single sample VCF and then to pass that in to the tool, but
Geraldine convinced me that this was a pain for users (because they usually have multi-sample VCFs).
Instead now you can pass in a multi-sample VCF and specify which sample's genotypes should be used
for the IUPAC encoding. Therefore the argument changed from '--useIUPAC' to '--use_IUPAC_sample NA12878'.
Stories:
https://www.pivotaltracker.com/story/show/66263868
Bug:
The problem was due to the way we were calculating the fix penalty of a large deletion or insertion. In this case we calculate the alignment likelihood of the portion
or read or haplotype deletion as the penalty of that deletion/insertion without going through the full pair-hmm process. For large events this resulted in a 0 in
in linear scale computations that ins transformed into an infinity in log scale.
Changes:
- Change to use log10 scale for calculate those penalties.
- Minor addition of .gitignore to hide ./public/external-example/target which is generated by the building process.
- SamPairUtils migrated in Picard r1737
- Revert IndelRealigner changes made in commit 4f4b85
-- Those changes were based on Picard revision 1722 to net/sf/picard/sam/SamPairUtil.java
-- Picard revision 1723 reverts these changes, so we also revert to match
This is currently my leading suspect for the cause of the
intermittent NoSuchElementException errors on master, since
the maven surefire plugin seems unable to handle errors in
TestNG DataProviders without blowing up.
This test is not, as I had initially thought, the cause of the
maven errors. Our master branch is failing intermittently
regardless of whether this test is enabled or disabled.
This reverts commit 45fc9ff515eec8d676b64a04fb34fb357492ff84.
This test passes when run individually, as part of the commit tests, or as
part of the package tests. However, when running the unit tests in isolation
it causes maven/surefire to throw a NoSuchElementException.
This is clearly a maven/surefire bug or configuration issue. I will re-enable
this test on a branch as Khalid and I try to work through it.
-Hide AWS downloader credentials in a private properties file
-Remove references to private ActiveRegion walker
Allows phone home functionality to be tested at release time
when we are running tests on the release jar.
1. Enable on-the-fly indexing for vcf.gz.
2. Handle on-the-fly indexing where file to be indexed is not a regular file, thus index should not be created.
3. Add method setProgressLogger to all SAMFileWriter implementations.
4. Revved picard to 1.109.1722
5. IndelRealigner md5s change because the MC tag is added to records now.
Fixed up and signed off by ebanks.
Package tests now hard coding just the gatk-framework tests jar, to include ONLY BaseTest, until the exclusions may be debugged.
Removing cofoja's annotation service from the package jars, to allow javac -cp <package>.jar.
Currently the best haplotypes are those that accumulate the largest ABSOLUTE edge *multiplicity* sum across their path in the assembly graph.
The edge *mulitplicity* is equal to the number of reads that expand through that edge, i.e. have a kmer that uniquely map to some vertex up-stream from the edge and the following base calls extend across that edge to vertices downstream from it.
Despite that it is obvious that higher multiplicties correlated with haplotype probability this criterion fails short in some regards of which the most relevant is:
As it is evaluated in condensed seq-graph (as supposed to uncompressed read-threading-graphs) it is bias to haplotypes that have more short-sequence vetices
( -> ATGC -> CA -> has worse score than -> A -> T -> G -> C -> C -> A ->). This is partly result of how we modify the edge multiplicities when we merge vertices from a linear chain.
This pull-request addresses the problem by changing to a new scoring schema based in likelihood estimates:
Each haplotype's likelihood can be calculated as the multiplication of the likelihood of "taking" its edges in the assembly graph. The likelihood of "taking" an edge in the assembly
graph is calculated as its multiplicity divide by the sum of multiplicity of edges that share the same source vertex.
This pull-request addresses the following stories:
https://www.pivotaltracker.com/story/show/66691418https://www.pivotaltracker.com/story/show/64319760
Change Summary:
1. Change to the new scoring schema.
2. Added a graph DOT printing code to KBestHaplotypeFinder in order to diagnose scoring.
3. Graph transformation have been modified in order to generate no 0-multiplicity edges. (Nevertheless the schema above should work with 0 edges assuming that they are in fact 0.5)
The maven shade plugin was eliminating a necessary class (IgnoreCookiesSpec)
when packaging the GATK/Queue. Work around this by telling maven to
always package all of commons-httpclient.
Enable it with the new --useIUPAC argument.
Added both unit and integration tests for the new functionality - and fixed up the
exising tests once I was in there.
-These tests are really integration tests for Queue rather than generalized
pipeline tests, so it makes sense to call them QueueTests.
-Rename test classes and maven build targets, and update shell scripts
to reflect new naming.
This module was causing failures during the release
packaging tests. After discussing with Khalid, we've
decided to disable it for now until a fix can be
developed.
C++ code has PAPI calls for reading hardware counters
Followed Khalid's suggestion for packing libVectorLoglessCaching into
the jar file with Maven
Native library part of git repo
1. Renamed directory structure from public/c++/VectorPairHMM to
public/VectorPairHMM/src/main/c++ as per Khalid's suggestion
2. Use java.home in public/VectorPairHMM/pom.xml to pass environment
variable JRE_HOME to the make process. This is needed because the
Makefile needs to compile JNI code with the flag -I<JRE_HOME>/../include (among
others). Assuming that the Maven build process uses a JDK (and not just
a JRE), the variable java.home points to the JRE inside maven.
3. Dropped all pretense at cross-platform compatibility. Removed Mac
profile from pom.xml for VectorPairHMM
Moved JNI_README
1. Added the catch UnsatisfiedLinkError exception in
PairHMMLikelihoodCalculationEngine.java to fall back to LOGLESS_CACHING
in case the native library could not be loaded. Made
VECTOR_LOGLESS_CACHING as the default implementation.
2. Updated the README with Mauricio's comments
3. baseline.cc is used within the library - if the machine supports
neither AVX nor SSE4.1, the native library falls back to un-vectorized
C++ in baseline.cc.
4. pairhmm-1-base.cc: This is not part of the library, but is being
heavily used for debugging/profiling. Can I request that we keep it
there for now? In the next release, we can delete it from the
repository.
5. I agree with Mauricio about the ifdefs. I am sure you already know,
but just to reassure you the debug code is not compiled into the library
(because of the ifdefs) and will not affect performance.
1. Changed logger.info to logger.warn in PairHMMLikelihoodCalculationEngine.java
2. Committing the right set of files after rebase
Added public license text to all C++ files
Added license to Makefile
Add package info to Sandbox.java
Conflicts:
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/DebugJNILoglessPairHMM.java
protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/JNILoglessPairHMM.java
protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java
public/VectorPairHMM/src/main/c++/.gitignore
public/VectorPairHMM/src/main/c++/LoadTimeInitializer.cc
public/VectorPairHMM/src/main/c++/LoadTimeInitializer.h
public/VectorPairHMM/src/main/c++/Makefile
public/VectorPairHMM/src/main/c++/Sandbox.cc
public/VectorPairHMM/src/main/c++/Sandbox.h
public/VectorPairHMM/src/main/c++/Sandbox.java
public/VectorPairHMM/src/main/c++/Sandbox_JNIHaplotypeDataHolderClass.h
public/VectorPairHMM/src/main/c++/Sandbox_JNIReadDataHolderClass.h
public/VectorPairHMM/src/main/c++/baseline.cc
public/VectorPairHMM/src/main/c++/define-double.h
public/VectorPairHMM/src/main/c++/define-float.h
public/VectorPairHMM/src/main/c++/define-sse-double.h
public/VectorPairHMM/src/main/c++/define-sse-float.h
public/VectorPairHMM/src/main/c++/headers.h
public/VectorPairHMM/src/main/c++/jnidebug.h
public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc
public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h
public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc
public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h
public/VectorPairHMM/src/main/c++/pairhmm-template-kernel.cc
public/VectorPairHMM/src/main/c++/pairhmm-template-main.cc
public/VectorPairHMM/src/main/c++/run.sh
public/VectorPairHMM/src/main/c++/shift_template.c
public/VectorPairHMM/src/main/c++/utils.cc
public/VectorPairHMM/src/main/c++/utils.h
public/VectorPairHMM/src/main/c++/vector_function_prototypes.h
-- throws UserException; added tests in PosteriorLikelihoodsUtilsUnitTests
Add error handling to CalculateGenotypePosteriors for cases where MLEAC>AN; add tests in PosteriorLikelihoodsUtilsUnitTests
Add unit tests to confirm that CalculateGenotypePosteriors has the ability to switch genotypes for four cases
Changes:
1. Addressed review comments on new K-best haplotype assembly graph finder.
2. Generalize KBestHaplotypeFinder to deal with multiple source and sink vertices.
3. Updated test to use KBestHaplotypeFinder instead of KBestPaths
4. Retired KBestPaths to the archive.
5. Small improvements to the code and documentation.
Story:
https://www.pivotaltracker.com/story/show/66238286
Changes:
1. Created a new k-best haplotype search implementation in class KBestHaplotypeFinder.
2. Changed HC code to use the new implementation.
This seems to fix the original problem without causing significant changes in outputs using some empirical data test cases
3. Moved haplotype's cigar calculation code from Path to CigarUtils; need that in order to gain independence from Path in some parts of the code.
In any case that seems like a more natural location for that functionality.
The GATK now fails with a user error if you try to run with a reduced bam.
(I added a unit test for that; everything else here is just the removal of all traces of RR)
PairHMMLikelihoodCalculationEngine.java to fall back to LOGLESS_CACHING
in case the native library could not be loaded. Made
VECTOR_LOGLESS_CACHING as the default implementation.
2. Updated the README with Mauricio's comments
3. baseline.cc is used within the library - if the machine supports
neither AVX nor SSE4.1, the native library falls back to un-vectorized
C++ in baseline.cc.
4. pairhmm-1-base.cc: This is not part of the library, but is being
heavily used for debugging/profiling. Can I request that we keep it
there for now? In the next release, we can delete it from the
repository.
5. I agree with Mauricio about the ifdefs. I am sure you already know,
but just to reassure you the debug code is not compiled into the library
(because of the ifdefs) and will not affect performance.
-- Keep a list of processed files in ArgumentTypeDescriptor.getRodBindingsCollection
-- Throw user exception if a file name duplicates one that was previously parsed
-- Throw user exception if the ROD list is empty
-- Added two unit tests to RodBindingCollectionUnitTest
public/VectorPairHMM/src/main/c++ as per Khalid's suggestion
2. Use java.home in public/VectorPairHMM/pom.xml to pass environment
variable JRE_HOME to the make process. This is needed because the
Makefile needs to compile JNI code with the flag -I<JRE_HOME>/../include (among
others). Assuming that the Maven build process uses a JDK (and not just
a JRE), the variable java.home points to the JRE inside maven.
3. Dropped all pretense at cross-platform compatibility. Removed Mac
profile from pom.xml for VectorPairHMM
Re-added import java.io.File for BamGatherFunction.
Other cleanup to resolve scala syntax warnings from intellij.
Moved Example UG script to from protected to public.
- This change means that BamGatherFunction will now have an @Output field for the BAM index, which will allow the bai to be deleted for intermediate functions
Signed-off-by: Khalid Shakir <kshakir@broadinstitute.org>
Bug uncovered by some untrimmed alleles in the single sample pipeline output.
Notice however does not fix the untrimmed alleles in general.
Story:
https://www.pivotaltracker.com/story/show/65481104
Changes:
1. Fixed the bug itself.
2. Fixed non-working tests (sliently skipped due to exception in dataProvider).
Note that this tool is still a work in progress and very experimental, so isn't 100% stable. Most of
the features are untested (both by people and by unit/integration tests) because Chris Hartl implemented
it right before he left, and we're going to need to add tests at some point soon. I added a first
integration test in this commit, but it's just a start.
The fixes include:
1. Stop having the genotyping code strip out AD values. It doesn't make sense that it should do this so
I don't know why it was doing that at all.
Updated GenotypeGVCFs so that it doesn't need to manually recover them anymore.
This also helps CalculateGenotypePosteriors which was losing the AD values.
Updated code in LeftAlignAndTrimVariants to strip out PLs and AD, since it wasn't doing that before.
Updated the integration test for that walker to include such data.
2. Chris was calling Math.pow directly on the normalized posteriors which isn't safe.
Instead, the normalization routine itself can revert back to log scale in a safe manner so let's use it.
Also, renamed the variable to posteriorProbabilities (and not likelihoods).
3. Have CGP update the AC/AF/AN counts after fixing GTs.
commit 5e73b94eed3d1fc75c88863c2cf07d5972eb348b
Merge: e12593a d04a585
Author: Nicholas Clarke <nc6@sanger.ac.uk>
Date: Fri Feb 14 09:25:22 2014 +0000
Merge pull request #1 from broadinstitute/checkpoint
SimpleTimer passes tests, with formatting
commit d04a58533f1bf5e39b0b43018c9db3302943d985
Author: kshakir <github@kshakir.org>
Date: Fri Feb 14 14:46:01 2014 +0800
SimpleTimer passes tests, with formatting
Fixed getNanoOffset() to offset nano to nano, instead of nano to seconds.
Updated warning message with comma separated numbers, and exact values of offsets.
commit e12593ae66a5e6f0819316f2a580dbc7ae5896ad
Author: Nicholas Clarke <nc6@sanger.ac.uk>
Date: Wed Feb 12 13:27:07 2014 +0000
Remove instance of 'Timer'.
commit 47a73e0b123d4257b57cfc926a5bdd75d709fcf9
Author: Nicholas Clarke <nc6@sanger.ac.uk>
Date: Wed Feb 12 12:19:00 2014 +0000
Revert a couple of changes that survived somehow.
- CheckpointableTimer,Timer -> SimpleTimer
commit d86d9888ae93400514a8119dc2024e0a101f7170
Author: Nicholas Clarke <nc6@sanger.ac.uk>
Date: Mon Jan 20 14:13:09 2014 +0000
Revised commits following comments.
- All utility merged into `SimpleTimer`.
- All tests merged into `SimpleTimerUnitTest`.
- Behaviour of `getElapsedTime` should now be consistent with `stop`.
- Use 'TimeUnit' class for all unit conversions.
- A bit more tidying.
commit 354ee49b7fc880e944ff9df4343a86e9a5d477c7
Author: Nicholas Clarke <nc6@sanger.ac.uk>
Date: Fri Jan 17 17:04:39 2014 +0000
Add a new CheckpointableTimerUnitTest.
Revert SimpleTimerUnitTest to the version before any changes were made.
commit 2ad1b6c87c158399ededd706525c776372bbaf6e
Author: Nicholas Clarke <nc6@sanger.ac.uk>
Date: Tue Jan 14 16:11:18 2014 +0000
Add test specifically checking behaviour under checkpoint/restart.
Slight alteration to the checkpointable timer based on observations
during the testing - it seems that there's a fair amount of drift
between the sources anyway, so each time we stop we resynchronise the
offset. Hopefully this should avoid gradual drift building up and
presenting as checkpoint/restart drift.
commit 1c98881594dc51e4e2365ac95b31d410326d8b53
Author: Nicholas Clarke <nc6@sanger.ac.uk>
Date: Tue Jan 14 14:11:31 2014 +0000
Should use consistent time units
commit 6f70d42d660b31eee4c2e9d918e74c4129f46036
Author: Nicholas Clarke <nc6@sanger.ac.uk>
Date: Tue Jan 14 14:01:10 2014 +0000
Add a new timer supporting checkpoint mechanisms.
The issue with this is that the current timer is locked to JVM nanoTime. This can be reset after
a checkpoint/restart and result in negative elapsed times, which causes an error.
This patch addresses the issue in two ways:
- Moves the check on timer information in GenomeAnalysisEngine.java to only occur if a time limit has been
set.
- Create a new timer (CheckpointableTimer) which keeps track of the relation between system and nano time. If
this changes drastically, then the assumption is that there has been a JVM restart owing to checkpoint/restart.
Any time straddling a checkpoint/restart event will not be counted towards total running time.
Signed-off-by: Khalid Shakir <kshakir@broadinstitute.org>
Updated path for output gatkdocs in nightly build script.
Removed patch in plugin manager that contained a workaround for gatkdocs running in the top level directory.
After extensive detective work, Joel determined that these tests were failing
due to changes in the implementation of Math.pow() in newer versions of
Java 1.7.
All GSA members should ensure that they're using a JDK that is at least
as current as the one in the Java-1.7 dotkit on the Broad servers
(build 1.7.0_51-b13).
This change should allow us to test that the GATK jar has been
correctly packaged at release time, by ensuring that only the
packaged jar + a few test-related dependencies are on the classpath
when tests are run.
Note that we still need to actually test that this works as intended
before we can make this live in the Bamboo release plan.
1. AD values now propogate up (they weren't before).
2. MIN_DP gets transferred over to DP and removed.
3. SB gets removed after FS is calculated.
Also, added a bunch of new integration tests for GenotypeGVCFs.
This tool will take any number of gVCFs and create a merged gVCF (as opposed to
GenotypeGVCFs which produces a standard VCF).
Added unit/integration tests and fixed up GATK docs.
Karthik Gururaj
Valentin Ruano-Rubio
Phillip Dexheimer
Michael McCowan
Ryan Poplin
kshakir
Carlos Borroto
Ami Levy-Moonshine
MauricioCarneiro
Joel Thibault
Kristian Cibulskis
Mike
Eric Banks
David Roazen
Laura Gauthier
Alec Wysoker
Khalid Shakir
Chris Whelan
pdexheimer
Nicholas Clarke
skashin
mghodrat