cc9477aedb
Minimal test for the multi-allelic reordering bug
2014-02-12 13:38:32 -05:00
1fcca8c5c0
Adding the filter field to the output of ROCCurveNA12878
2014-02-12 12:46:30 -05:00
6facf695ab
Merge pull request #506 from broadinstitute/eb_quick_fixes_to_single_sample_pipeline
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Several improvements to the single sample combining steps.
2014-02-12 11:30:48 -05:00
300b474c96
Several improvements to the single sample combining steps.
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1. updated QualByDepth not to use AD-restricted depth if it is zero.
Added unit test this change.
2. Fixed small bug in CombineGVCFs where spanning deletions were not being treated consistently throughout.
Added test for this situation.
3. Make sure GenotypeGVCFs puts in the required headers.
Updated test files to make sure this is covered.
4. Have GenotypeGVCFs propagate up the MLEAC/AF (which were getting clobbered out).
Tests updated to account for this.
2014-02-12 10:15:12 -05:00
ff8c9575b0
Merge pull request #505 from broadinstitute/ks_build_na12878kb-utils
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Ported na12878kb.jar assembly from Ant's build.xml to Maven
2014-02-12 10:10:52 -05:00
403ce7bfb7
Ported na12878kb.jar assembly from Ant's build.xml to Maven at request of jsilter
2014-02-12 06:01:32 +08:00
3cfcfa4fa0
Merge pull request #504 from broadinstitute/dr_enable_kb_tests_in_maven
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Add ability to run *KnowledgeBaseTests to maven
2014-02-11 15:32:24 -05:00
95e1402d21
Add ability to run *KnowledgeBaseTests to maven
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Run with: mvn verify -Dsting.knowledgebasetests.skipped=false
2014-02-11 14:08:24 -05:00
cc9a3b68fc
Merge pull request #503 from broadinstitute/ks_maven_gatkdocs_patch
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Patched PluginManager to ignore null classes
2014-02-11 13:28:24 -05:00
96e29d3d94
Merge pull request #500 from broadinstitute/eb_make_qd_more_robust
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Adding smarts to the QD annotation
2014-02-11 12:57:50 -05:00
303a60c8c6
Adding smarts to the QD annotation:
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when the AD annotation is present for a given genotype then we only use its depth for QD if the variant depth > 1.
Added new unit tests for QualByDepth.
2014-02-11 12:56:49 -05:00
1666bb7e3a
Patched PluginManager to ignore null classes, that will allow gatkdocs to build successfully when running from the source root directory, due to its hardcoded paths.
2014-02-12 00:48:58 +08:00
b33d9d9105
Merge pull request #502 from broadinstitute/eb_make_combine_gvcfs_faster
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Refactoring of CombineGVCFs to make it run a lot faster.
2014-02-11 09:03:16 -05:00
2e36dd9001
Refactoring of CombineGVCFs to make it run a lot faster.
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Creating new VariantContexts each time we broke up a block was very expensive because we break up
blocks so often. Also, calling into GATKVariantContextUtils.simpleMerge was really hurting performance.
MD5 changes because we no longer propogate any INFO fields (except for END) for reference blocks; the tests
have the now unused BLOCK_SIZE field that now get dropped.
2014-02-11 03:18:52 -05:00
316501b32e
Fixed denominator in profiling
2014-02-10 10:11:03 -08:00
d081c19178
Minor: added support in C++ sandbox to choose implementation and check
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from command line
2014-02-09 18:05:35 -08:00
b81494b704
Merge pull request #499 from broadinstitute/eb_fix_ad_updates
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Fixed bug in generating AD values when new alleles are present for genot...
2014-02-09 17:55:00 -05:00
abb67cfa5e
Fixed bug in generating AD values when new alleles are present for genotpying GVCFs.
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This was a dumb mistake that wasn't well tested (but is now).
2014-02-09 15:15:19 -05:00
c2a2484a18
Merge pull request #498 from broadinstitute/ks_delete_pricard_private
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Removed use of picard private.
2014-02-09 10:27:48 -05:00
12bb6fd361
Removed use of picard private.
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Updated picard-maven script to tag locally modified builds with -SNAPSHOT.
Removed old picard jars.
2014-02-09 17:08:52 +08:00
597cc88f33
Merge pull request #497 from broadinstitute/eb_remove_ac0_alleles_PT65118652
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Removing parameters that were incorrectly copied over from RegenotypeVariants
2014-02-08 23:46:23 -05:00
abef6cfcb6
Removing parameters that were incorrectly copied over from RegenotypeVariants.
2014-02-08 23:44:32 -05:00
e9189cd471
Merge pull request #496 from broadinstitute/eb_remove_test_for_blocksize
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Removing the test for BLOCK_SIZE since we no longer emit it
2014-02-08 21:29:02 -05:00
659a9f0e79
Removing the test for BLOCK_SIZE since we no longer emit it
2014-02-08 21:28:07 -05:00
a33d7ace11
Merge pull request #495 from broadinstitute/ks_increase_scala_memory
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Made scala.maxmemory an argument, and defaulted it to 1g.
2014-02-08 21:13:26 -05:00
4decb49ecb
Merge pull request #494 from broadinstitute/vrr_reference_model_nocall_bugfix
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Fixed nocall (./.) without PLs bug in GVCF output
2014-02-08 21:12:45 -05:00
4e0f7521f2
Made scala.maxmemory an argument, and defaulted it to 1g.
2014-02-09 09:24:44 +08:00
a03d83579b
Matrices in baseline C++ (no vector) implementation of PairHMM are now
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allocated on heap using "new". Stack allocation led to program crashes
for large matrix sizes.
2014-02-07 23:22:05 -08:00
bf630abe88
Fixed nocall (./.) without PLs bug in GVCF output
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Story:
https://www.pivotaltracker.com/story/show/65388246
Additional changes and notes:
1. The fix consist in forcing the output of all PLs by setting the standard flag for that '-allSitePLs'.
2. BP_RESOLUTION was handled differently to GVCF in some aspect that should be common. That has been fixed.
2014-02-07 19:30:26 -05:00
20a46e4098
Check only for SSE 4.1 (rather than SSE 4.2) when trying to use the SSE
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implementation of PairHMM
2014-02-07 15:19:55 -08:00
dc44b64ad8
1. Added support for building the PairHMM vector library into build.xml.
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The library is compiled using makefile and copied into the directory:
build/java/classes/org/broadinstitute/sting/utils/pairhmm/
2. Bundled the library into StingUtils.jar. Unpacked and loaded at
runtime without the need to set java.library.path
Caveats:
Platform independence has probably been thrown out of the window.
Assumptions:
a. make command exists at /usr/bin/make
b. rsync command exists at /usr/bin/rsync
c. icc is in the PATH of the user
2014-02-07 13:13:59 -08:00
8c922be684
Merge pull request #491 from broadinstitute/eb_get_AD_back_from_gvcfs
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Fixed up some of the genotype-level annotations being propogated in the ...
2014-02-07 12:50:01 -05:00
d689f61005
Fixed up some of the genotype-level annotations being propogated in the single sample HC pipeline.
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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.
2014-02-07 12:47:54 -05:00
0a1385a4d9
Merge pull request #493 from broadinstitute/eb_fix_failing_merge_for_tim
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The UG engine can return a null VC if there are tons of alt alleles, cau...
2014-02-07 12:43:40 -05:00
67ed0d2403
The UG engine can return a null VC if there are tons of alt alleles, causing Tim's merge jobs to fail.
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Pushing the null check up so that it doesn't error out in such cases.
2014-02-07 12:41:20 -05:00
335483bb53
Merge pull request #492 from broadinstitute/eb_fix_failing_unit_tests
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Fixing failing unit tests
2014-02-07 12:25:10 -05:00
db68d3fa10
Fixing failing unit tests
2014-02-07 12:24:14 -05:00
8e87e083ff
Merge pull request #490 from broadinstitute/vrr_reference_model_unsorted_records_bugfix
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Fixed out of order non-variant gVCF entries when trimming is active.
2014-02-07 12:21:12 -05:00
4a3c8e68fa
Fixed out of order non-variant gVCF entries when trimming is active.
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Story:
https://www.pivotaltracker.com/story/show/65319564
2014-02-07 11:03:26 -05:00
369fbd4439
Merge pull request #489 from broadinstitute/eb_hierarchical_gvcf_merger
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Eb hierarchical gvcf merger
2014-02-07 08:50:39 -05:00
eb463b505d
Remove a whole bunch of unused annotations from gVCF output.
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AC,AF,AN,FS,QD - they'll all be recomputed later.
BLOCK_SIZE and MIN_GQ were not necessary.
I also made the StrandBiasBySample annotation forced on when in gVCF mode.
It turns out that its output wasn't compatible with BCF so I patched it (and the variant jar too).
2014-02-07 08:49:36 -05:00
2648219c42
Implementation of a hierarchical merger for gVCFs, called CombineGVCFs.
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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.
2014-02-07 08:49:18 -05:00
7815c30df8
Adding comments to pairhmm-template-kernel
2014-02-06 20:13:06 -08:00
b729fc0136
1. Split main JNI function into initializeTestcases, compute_testcases
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and releaseReads
2. FTZ enabled
3. Cleaner profiling code
2014-02-06 14:35:32 -08:00
71b47a6148
Rename CombineReferenceCalculationVariants to GenotypeGVCFs
2014-02-06 15:46:19 -05:00
b2b44c335f
Merge pull request #488 from broadinstitute/ks_mvn_serial_test_updates
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Ks mvn serial test updates
2014-02-06 15:12:08 -05:00
166f91d698
Merge branch 'test_branch'
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Conflicts:
public/c++/VectorPairHMM/LoadTimeInitializer.cc
public/c++/VectorPairHMM/pairhmm-1-base.cc
public/c++/VectorPairHMM/utils.cc
public/c++/VectorPairHMM/utils.h
Merged test_branch with intel_pairhmm
2014-02-06 11:18:18 -08:00
fab6f57e97
1. Enabled FTZ in LoadTimeInitializer.cc
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2. Added Sandbox.java for testing
3. Moved compute to utils.cc (inside library)
4. Added flag for disabling FTZ in Makefile
2014-02-06 11:01:33 -08:00
78642944c0
1. Moved break statement in utils.cc to correct position
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2. Tested sandbox with regions
3. Lots of profiling code from previous commit exists
2014-02-06 09:32:56 -08:00
b21c35482e
Packages link private/testdata, so that mvn test -Dsting.serialunittests.skipped=false works.
2014-02-06 08:25:38 -05:00
Joel Thibault
Ryan Poplin
Eric Banks
Khalid Shakir
droazen
Karthik Gururaj
Valentin Ruano-Rubio
mghodrat