Passing implementation of custom ploidy regions in HaplotypeCaller #8609
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Finish changes to HaplotypeCaller to add ploidy-regions flag allowing variable ploidy Change IntervalFileFeature interface to NamedFeature for htsjdk dependency Address comments for draft PR Make a few changes and refactors based on comments Add some tests and small tweaks
* Introduced a new class MulitPloidyGenotyperCache which keeps track of multiple GenotypingEngines that have different ploidy values. * minor refactoring in related classes * removed an unused type parameter from GenotypingEngine
Remove old fields from HCE Change data source to FeatureInput Remove old commented code; add test arg copy sync deeper fields
This reverts commit a40ba3e.
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@lbergelson Should this PR be into master, or into @rickymagner 's branch? |
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So I just updated one of the newer tests, and now all of the tests for HaplotypeCaller seem to be passing locally. The previous commits updating the copy code were preserved when Louis reverted, so there were basically no changes I had to make to get this "working." That does leave us with one question now: When looking into this a little with James and Louis earlier, we realized that the code for setting up the ActiveRegionGenotyper uses a weird partial copy of the standard CLI args method that has existed in the code for whoever knows how long. Conceptually this seems like a bad idea, but changing it now would possibly cause some older tests to fail, if they were based on this faulty method reasoning. Should we try to merge the PR as it is now, with all tests passing, and hopefully consistency with previous behavior, or try to update the logic around this genotyper as well at the same time? It's possible we can try to address the latter point as well at some point in the future when we try to get Louis's refactor code actually working. Maybe there could be some quarter goal around a HaplotypeCaller code revamp sometime inspired by some of these ideas? |
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And @droazen I think it's correct for the target of this PR to be master. After all, the old PR was always technically just a draft. 😄 |
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@rickymagner I'd recommend postponing any further refactoring for future PRs post-release, in the interests of checkpointing this feature -- assuming that we're confident the feature works as intended and there are no side effects in other HaplotypeCaller codepaths. If the new argument is not already marked as Experimental, perhaps it should be until it's seen some more usage? |
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I'd be OK with adding some sort of experimental tag, but I'm not sure where to put it. Does that goes in the docs or somewhere in the code to post a warning to the log? I think the new tests should cover that it's working as intended. There is definitely room for future work (e.g. paying closer attention around the boundaries, the refactoring ideas, etc), but for now the docs should describe the expected behavior well. |
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@rickymagner I think as long as you trust the test this is probably good to go in. I have some ideas about improvements but I'd say we should leave that for another pr. |
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#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrotOrchestrated.gatk_docker, ) |
🥕CARROT🥕 run startedTest: HaplotypeCaller CARROT Regression Tests | Status: buildingRun: HaplotypeCaller CARROT Regression Tests_run_2023-12-09 01:13:16.103236135 UTC Full details
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🥕CARROT🥕 run finishedTest: HaplotypeCaller CARROT Regression Tests | Status: eval_failedRun: HaplotypeCaller CARROT Regression Tests_run_2023-12-09 01:13:16.103236135 UTC Full details
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],
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]
},
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"created_at": "2023-12-09T01:13:16.103312",
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"finished_at": "2023-12-09T10:01:23.242",
"results": null,
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}
|
|
#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrotOrchestrated.gatk_docker, ) |
🥕CARROT🥕 run startedTest: HaplotypeCaller CARROT Regression Tests | Status: buildingRun: HaplotypeCaller CARROT Regression Tests_run_2023-12-09 19:10:16.577655639 UTC Full details
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},
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},
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"BenchmarkVCFsHeadToHeadOrchestrated.NIST_controlVcf": "test_output:VariantCallingCarrotOrchestrated.NIST_control_vcf",
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"BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalVcf": "test_output:VariantCallingCarrotOrchestrated.NIST_output_vcf",
"BenchmarkVCFsHeadToHeadOrchestrated.NIST_evalVcfIndex": "test_output:VariantCallingCarrotOrchestrated.NIST_output_vcf_index",
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"BenchmarkVCFsHeadToHeadOrchestrated.refDict": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.dict",
"BenchmarkVCFsHeadToHeadOrchestrated.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
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],
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},
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}
|
🥕CARROT🥕 run finishedTest: HaplotypeCaller CARROT Regression Tests | Status: eval_failedRun: HaplotypeCaller CARROT Regression Tests_run_2023-12-09 19:10:16.577655639 UTC Full details
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]
},
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},
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}
|
|
The Carrot tests are failing due to issues with R dependencies unrelated to this PR. Since it might take a day to fix, we are debating whether we're comfortable merging this without seeing the full-scale Carrot HaplotypeCaller test results. |
|
Looks like there was an R error in Carrot. Fortunately the actual meat of the Carrot test ran to completion (for the CHM) I have also checked that this matches for the exome and the NIST sample. I would say that these samples are exactly matching in terms of their VCFeval output and thus we can be confident that this branch did not break the standard pipeline path and we can call this 👍. |
|
#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrotOrchestrated.gatk_docker, ) |
🥕CARROT🥕 run startedTest: HaplotypeCaller CARROT Regression Tests | Status: buildingRun: HaplotypeCaller CARROT Regression Tests_run_2023-12-18 13:56:16.652443526 UTC Full details
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}
|
🥕CARROT🥕 run finishedTest: HaplotypeCaller CARROT Regression Tests | Status: eval_failedRun: HaplotypeCaller CARROT Regression Tests_run_2023-12-18 13:56:16.652443526 UTC Full details
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"BenchmarkVCFsHeadToHeadOrchestrated.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
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"BenchmarkVCFsHeadToHeadOrchestrated.referenceVersion": "HG38",
"BenchmarkVCFsHeadToHeadOrchestrated.stratIntervals": [
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],
"BenchmarkVCFsHeadToHeadOrchestrated.stratLabels": [
"HCR",
"LCR"
]
},
"eval_options": {
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},
"test_cromwell_job_id": "87fbbde1-241f-43b3-be7d-78d4dd3c79cc",
"eval_cromwell_job_id": "618c4924-839d-4b4b-8cc4-c01b86f36d0b",
"created_at": "2023-12-18T13:56:16.652540",
"created_by": null,
"finished_at": "2023-12-18T17:54:34.690",
"results": null,
"errors": null
}
|
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@rickymagner