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Rewrite haplotype construction methods in PDHapComputationEngine #8367

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merged 3 commits into from
Jul 27, 2023
Merged

Rewrite haplotype construction methods in PDHapComputationEngine #8367

merged 3 commits into from
Jul 27, 2023

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davidbenjamin
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@davidbenjamin davidbenjamin commented Jun 15, 2023 •
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@jamesemery Here's another fun one, again no change in output but significant refactoring of constructHaplotypeFromVariants and createNewPDHaplotypeFromEvents.

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gatk-bot commented Jun 15, 2023 •
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Github actions tests reported job failures from actions build 5275320578
Failures in the following jobs:

Test Type JDK Job ID Logs
unit 17.0.6+10 5275320578.12 logs
unit 17.0.6+10 5275320578.1 logs

@davidbenjamin davidbenjamin requested a review from jamesemery June 15, 2023 12:32
jamesemery
jamesemery reviewed Jun 16, 2023
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I need to keep staring at this.... you should take a look at the unit tests for this class and consider if its worth adding some more test cases

.../hellbender/tools/walkers/haplotypecaller/PartiallyDeterminedHaplotypeComputationEngine.java Show resolved Hide resolved
.../hellbender/tools/walkers/haplotypecaller/PartiallyDeterminedHaplotypeComputationEngine.java Show resolved Hide resolved
.../hellbender/tools/walkers/haplotypecaller/PartiallyDeterminedHaplotypeComputationEngine.java Outdated Show resolved Hide resolved
.../hellbender/tools/walkers/haplotypecaller/PartiallyDeterminedHaplotypeComputationEngine.java Outdated Show resolved Hide resolved
.../hellbender/tools/walkers/haplotypecaller/PartiallyDeterminedHaplotypeComputationEngine.java Outdated Show resolved Hide resolved
@davidbenjamin davidbenjamin force-pushed the db_dragen_construct_haplotype_from_events branch from f215fa1 to efa50ce Compare June 26, 2023 18:45
@davidbenjamin davidbenjamin force-pushed the db_dragen_construct_haplotype_from_events branch from efa50ce to fdd365b Compare June 27, 2023 20:48
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Back to you, @jamesemery

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jamesemery approved these changes Jul 25, 2023
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looks good, very minor comments but otherwise i see no reason to keep blocking this

.../hellbender/tools/walkers/haplotypecaller/PartiallyDeterminedHaplotypeComputationEngine.java Outdated
// NOTE: we set this AFTER generating the event maps because hte event map code above is being generated from the ref hap so this offset will cause out of bounds errors
outHaplotype.setAlignmentStartHapwrtRef(refHap.getAlignmentStartHapwrtRef()); //TODO better logic here
result.setAlignmentStartHapwrtRef(refHap.getAlignmentStartHapwrtRef()); //TODO better logic here
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comments above

.../hellbender/tools/walkers/haplotypecaller/PartiallyDeterminedHaplotypeComputationEngine.java Show resolved Hide resolved
.../hellbender/tools/walkers/haplotypecaller/PartiallyDeterminedHaplotypeComputationEngine.java Outdated Show resolved Hide resolved
@davidbenjamin davidbenjamin merged commit 5bd612b into master Jul 27, 2023
@davidbenjamin davidbenjamin deleted the db_dragen_construct_haplotype_from_events branch July 27, 2023 22:06
rickymagner pushed a commit that referenced this pull request Nov 28, 2023
@davidbenjamin @rickymagner
Rewrite haplotype construction methods in PDHapComputationEngine (#8367)
6525d9e
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