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Solves issue 7153 #7154

Merged
merged 1 commit into from
Apr 8, 2021
Merged

Solves issue 7153 #7154

merged 1 commit into from
Apr 8, 2021

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vruano
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@vruano vruano commented Mar 19, 2021

involving "zombie" likelihoods from past removed evidences being assigned to new appended evidences in AlleleLikelihoods.

Refactor and clean some code as well.

@vruano vruano requested a review from davidbenjamin March 19, 2021 04:29
@vruano vruano mentioned this pull request Mar 19, 2021
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davidbenjamin approved these changes Mar 30, 2021
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Looks good, just wondering about removing public in a few places.

...java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleLikelihoodMatrixMapper.java Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/utils/genotyper/LikelihoodMatrix.java Show resolved Hide resolved
@vruano vruano force-pushed the vrr_bug7153_allele_likelihoods_ghost_lk_values branch from c107710 to b6693fe Compare March 31, 2021 03:28
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@vruano Good to merge whenever you want!

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Travis reported job failures from build 33424
Failures in the following jobs:

Test Type JDK Job ID Logs
variantcalling openjdk8 33424.4 logs

@vruano vruano force-pushed the vrr_bug7153_allele_likelihoods_ghost_lk_values branch from b6693fe to 7b1ea37 Compare March 31, 2021 05:19
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gatk-bot commented Mar 31, 2021 •
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Travis reported job failures from build 33426
Failures in the following jobs:

Test Type JDK Job ID Logs
unit openjdk11 33426.13 logs
unit openjdk8 33426.3 logs
variantcalling openjdk8 33426.4 logs

@vruano vruano force-pushed the vrr_bug7153_allele_likelihoods_ghost_lk_values branch 2 times, most recently from 3d509e3 to cb16f72 Compare April 1, 2021 14:15
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gatk-bot commented Apr 2, 2021

Travis reported job failures from build 33490
Failures in the following jobs:

Test Type JDK Job ID Logs
variantcalling openjdk8 33490.4 logs

@vruano vruano force-pushed the vrr_bug7153_allele_likelihoods_ghost_lk_values branch from 58c8bac to a46cba9 Compare April 4, 2021 10:52
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gatk-bot commented Apr 4, 2021 •
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Travis reported job failures from build 33523
Failures in the following jobs:

Test Type JDK Job ID Logs
integration openjdk11 33523.12 logs
integration openjdk8 33523.2 logs

@vruano vruano force-pushed the vrr_bug7153_allele_likelihoods_ghost_lk_values branch from 5257f2f to 0c445eb Compare April 5, 2021 02:43
@vruano vruano requested a review from droazen April 5, 2021 02:45
vruano
vruano commented Apr 5, 2021
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src/test/java/org/broadinstitute/hellbender/utils/genotyper/AlleleLikelihoodsUnitTest.java Outdated

private static final SAMFileHeader SAM_HEADER = ArtificialReadUtils.createArtificialSamHeader(10, 0, 1000);
private static final GenomeLocParser locParser = new GenomeLocParser(SAM_HEADER.getSequenceDictionary());

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extra blank line

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gatk-bot commented Apr 5, 2021

Travis reported job failures from build 33528
Failures in the following jobs:

Test Type JDK Job ID Logs
integration openjdk11 33528.12 logs

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gatk-bot commented Apr 5, 2021 •
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Travis reported job failures from build 33531
Failures in the following jobs:

Test Type JDK Job ID Logs
integration openjdk11 33531.12 logs
integration openjdk8 33531.2 logs

@vruano
Solves issue 7153 involing "zombie" likelihods from past removed evid…
6eb8c22 
…ences being assigned

to new appended evidences in AlleleLikelihoods.

Refactor and clean some code
@vruano vruano force-pushed the vrr_bug7153_allele_likelihoods_ghost_lk_values branch from 06a6e12 to 6eb8c22 Compare April 8, 2021 04:02
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vruano commented Apr 8, 2021

Squashing and rebasing, will merge as soon as test pass.

@vruano vruano removed the request for review from droazen April 8, 2021 04:03
@vruano vruano assigned vruano and unassigned davidbenjamin Apr 8, 2021
@vruano vruano merged commit 69f4fc4 into master Apr 8, 2021
@vruano vruano deleted the vrr_bug7153_allele_likelihoods_ghost_lk_values branch April 8, 2021 13:14
@vruano vruano restored the vrr_bug7153_allele_likelihoods_ghost_lk_values branch April 8, 2021 13:15
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