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 is needed so the ref model pipeline can cut down to sites-only files without losing these useful statistics.
-- Added new unit test to test this info field annotation.
-- GenotypeGVCF integration tests change because new annotations are present in the output
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
Story:
- https://www.pivotaltracker.com/story/show/67601310
Change:
- Unless recover-danging-heads is active, the threading starting location policy is the original one. i.e. just at already existing unique kmer vertices.
Tests:
- HaplotypeCallerIntegrationTest#testMissingKeyAlternativeHaplotypesBugFix
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.
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)
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.
-- All the provided alleles are added to the assembly graph as potential haplotypes but they aren't forcibly genotyped like in GGA mode.
-- Added integration test for this mode
-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.
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
Eric Banks
Valentin Ruano-Rubio
Ryan Poplin
MauricioCarneiro
Joel Thibault
David Roazen
Alec Wysoker
Laura Gauthier
Bertrand Haas
Karthik Gururaj