Unified HaplotypeCaller's force-calling mode with Mutect2's #6090
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| public FeatureInput<VariantContext> alleles; | ||
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| @Advanced | ||
| @Argument(fullName = "genotype-filtered-alleles", doc = "Whether to force genotype even filtered alleles", optional = true) |
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I would say "Force genotyping of filtered alleles included in the resource specified by --alleles"
| if ( assemblyArgs.ggaExtension < 0) { | ||
| throw new CommandLineException.BadArgumentValue("maxGGAAREExtension", "" + assemblyArgs.ggaExtension + "< 0"); | ||
| if ( assemblyArgs.extension < 0) { | ||
| throw new CommandLineException.BadArgumentValue("maxDiscARExtension", "" + assemblyArgs.extension + "< 0"); |
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The diff for this file is so beautiful. <3 I'm glad you took out all the GGA special casing.
| @@ -1820,5 +1822,6 @@ public static boolean isUnmixedMnpIgnoringNonRef(final VariantContext vc) { | |||
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| return true; | |||
| } | |||
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It's not obvious why there are two new imports, but no new code.
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That was diplomatic.
| .collect(Collectors.toMap(vc -> vc.getStart(), vc -> vc.getAlternateAlleles())); | ||
| for (final VariantContext vc : new FeatureDataSource<VariantContext>(forceCallingVcf)) { | ||
| final List<Allele> altAllelesAtThisLocus = altAllelesByPosition.get(vc.getStart()); | ||
| vc.getAlternateAlleles().forEach(a -> Assert.assertTrue(altAllelesAtThisLocus.contains(a))); |
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Thanks for this improved test.
| @@ -32,7 +32,6 @@ | |||
| 20 10004094 . A T . . . GT 0|1 | |||
| 20 10004769 . TAAAACTATGC T . . . GT 0|1 | |||
| 20 10004771 . A T . . . GT 0|1 | |||
| 20 10006819 . AAAAC T . . . GT 0|1 | |||
| 20 10006819 . AAAAC A . . . GT 0|1 | |||
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It looks like these are fixes with respect to the proper reference base?
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That's right. The old GGA mode didn't care if the -alleles vcf was invalid.
| // then we may need to trim the alleles (because the original VariantContext may have had to pad at the end). | ||
| if ( outputAlleles.size() != vc.getAlleles().size() && !limitedContext ) // limitedContext callers need to handle allele trimming on their own to keep their alleles in sync | ||
| { | ||
| vcCall = GATKVariantContextUtils.reverseTrimAlleles(vcCall); |
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Where did the trimming go?
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We had above:
final boolean limitedContext = features == null || refContext == null || rawContext == null || stratifiedContexts == null;
In every invocation of this method (which I think I cleaned up in this PR) all of these things were null and so limtiedContext was inevitable true. Hence the && !limitedContext prevented this reverse trimming code from ever being reached.
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And don't worry, M2 and HC still properly trim alleles. In fact, M2 already has an integration test to make sure we output a parsimonious allele representation even after indels that miss the tumor lod threshold are invisibly dropped.
| @@ -389,7 +338,9 @@ private OutputAlleleSubset calculateOutputAlleleSubset(final AFCalculationResult | |||
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| //it's possible that the upstream deletion that spanned this site was not emitted, mooting the symbolic spanning deletion allele | |||
| final boolean isSpuriousSpanningDeletion = GATKVCFConstants.isSpanningDeletion(allele) && !isVcCoveredByDeletion(vc); | |||
| final boolean toOutput = (isPlausible || forceKeepAllele(allele) || isNonRefWhichIsLoneAltAllele) && !isSpuriousSpanningDeletion; | |||
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| //TODO: force-clling logic goes here | |||
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Whoops, that had already been addressed. Fixed.
| } | ||
| // if the site was down-sampled, record that fact | ||
| if ( !limitedContext && rawContext.hasPileupBeenDownsampled() ) { | ||
| attributes.put(GATKVCFConstants.DOWNSAMPLED_KEY, true); |
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I have never ever seen data that has this key. I'm glad you're removing any mention of it.
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More unreachable code due to limitedContext always being true.
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Addressed comments and beefed-up test coverage. Back to @ldgauthier. |
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@ldgauthier Fresh rebase post-deletion of old qual. |
| @@ -125,4 +130,11 @@ public ReadThreadingAssembler createReadThreadingAssembler() { | |||
| @Argument(fullName = MAX_MNP_DISTANCE_LONG_NAME, shortName = MAX_MNP_DISTANCE_SHORT_NAME, | |||
| doc = "Two or more phased substitutions separated by this distance or less are merged into MNPs.", optional = true) | |||
| public int maxMnpDistance = getDefaultMaxMnpDistance(); | |||
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| @Argument(fullName= FORCE_CALL_ALLELES_LONG_NAME, doc="The set of alleles for which to force genotyping regardless of evidence", optional=true) | |||
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There are a bunch of places where the variables or test names or whatever say force call, but the arg doc here says force genotyping. Very minor nit to pick, but it would be good to be consistent.
@ldgauthier as we discussed.