GnarlyGenotyper tech debt #6075
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@ldgauthier Could you please rebase this branch onto the latest master, so that we can see whether tests pass? |
AnnotationUtils.isAlleleSpecific()"
--floor-blocks HaplotypeCaller arg" Also clarified beta status for GVCF mode just for Mutect2
GenomicsDB options
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| return true; | ||
| } | ||
| if (annotation instanceof AS_StandardAnnotation) { | ||
| if (annotation instanceof AlleleSpecificAnnotation) { |
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This branch references the new AlleleSpecificAnnotation interface in several places, but does not seem to actually introduce it. Maybe you just forgot to git add it?
| if (hcArgs.floorBlocks && !emitReferenceConfidence()) { | ||
| throw new UserException(HaplotypeCallerArgumentCollection.OUTPUT_BLOCK_LOWER_BOUNDS + " refers to GVCF blocks," + | ||
| " so reference confidence mode (" + AssemblyBasedCallerArgumentCollection.EMIT_REFERENCE_CONFIDENCE_LONG_NAME + | ||
| ") must be specified."); |
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You included this check twice here.
| @@ -371,6 +372,43 @@ else if (!vc.getAlternateAllele(0).equals(Allele.NON_REF_ALLELE)){ //there | |||
| } | |||
| } | |||
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| /* | |||
| * Test that in VCF mode we're consistent with past GATK4 results | |||
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Comment does not match the test. Should be something like "Test the --floor-blocks argument."
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| final ArgumentsBuilder args = new ArgumentsBuilder().addInput(new File(inputFileName)) | ||
| .addReference(new File(referenceFileName)) | ||
| .addInterval(new SimpleInterval("20:10000000-10100000")) |
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This interval might be unnecessarily large for this test -- could you shrink it down?
| return true; | ||
| } | ||
| if (annotation instanceof AS_StandardAnnotation) { | ||
| if (annotation instanceof AlleleSpecificAnnotation) { | ||
| return true; | ||
| } | ||
| return false; |
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return annotation instanceof AlleleSpecificAnnotation; would be more compact
| * This is similar to the HaplotypeCaller reference confidence/GVCF mode. See https://software.broadinstitute.org/gatk/documentation/article.php?id=4017 for information about GVCFs. | ||
| * The reference confidence mode makes it possible to emit a per-bp or summarized confidence estimate for a site being strictly homozygous-reference. | ||
| * See https://software.broadinstitute.org/gatk/documentation/article.php?id=4017 for information about GVCFs. | ||
| * This is a BETA FEATURE for Mutect2 similar to the HaplotypeCaller reference confidence/GVCF mode. |
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Recommend rewording slightly to put "Mutect2" at the start of the sentence before the word "BETA": "For Mutect2, this is a BETA feature that functions similarly to the HaplotypeCaller reference confidence/GVCF mode."
| */ | ||
| @Advanced | ||
| @Argument(fullName="emit-ref-confidence", shortName="ERC", doc="(BETA feature) Mode for emitting reference confidence scores", optional = true) | ||
| @Argument(fullName=EMIT_REFERENCE_CONFIDENCE_LONG_NAME, shortName="ERC", doc="Mode for emitting reference confidence scores (BETA for Mutect2)", optional = true) |
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(BETA for Mutect2) -> (For Mutect2, this is a BETA feature)
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Sorry, that was sloppy. I expect that now it builds. Addressed all the review comments. |
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Looks like travis failed with an out-of-memory error (exit code 137) in gradle. @lbergelson was investigating this error earlier, and we thought we'd fixed it... |
Addressing @droazen 's outstanding comments from #4947
Also closes #5988