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.
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>
This commit consists of 2 main changes:
1. When the strand table gets too large, we normalize it down to values that are more reasonable.
2. We don't include a particular sample's contribution unless the total ref and alt counts are at least 2 each;
this is a heuristic method for dealing only with hets.
MD5s change as expected.
Hopefully we'll have a more robust implementation for GATK 3.1.
The slicePrefix method functionality was broken.
Story:
https://www.pivotaltracker.com/story/show/64595624
Changes:
1. Fixed the bug.
2. Added unit test to check on the method functionality.
3. Added a integration test to verify the bug has been fixed in a empirical data reprudible case.
Story:
https://www.pivotaltracker.com/s/projects/1007536
Changes:
1. HC's GenotypingEngine now invokes reverseAlleleTrimming on GVCF variant output lines.
2. GenotypeGVCFs also reverse trim after regenotyping as some alt. alleles are dropped (observed in real-data).
The writer was never resetting the pointer to the end of the last non-ref VariantContext that it saw.
This was fine except when it jumped to a new contig - and a lower position on that contig - where it
thought that it was still part of that previous non-ref VariantContext so wouldn't emit a reference
block. Therefore, ref blocks were missing from the beginnings of all chromosomes (except chr1).
Added unit test to cover this case.
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).
This script publishes GATK/Queue jars for internal GSA use to the following locations
whenever tests pass:
/humgen/gsa-hpprojects/GATK/private_unstable_builds/GenomeAnalysisTK_latest_unstable.jar
/humgen/gsa-hpprojects/Queue/private_unstable_builds/Queue_latest_unstable.jar
These jars include private code, and so are for internal use only.
Karthik Gururaj
Eric Banks
Khalid Shakir
pdexheimer
kshakir
droazen
Valentin Ruano Rubio
Ryan Poplin