single sample fast mode for qual is HC isActive #6343
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ldgauthier
approved these changes
Jan 6, 2020
| * for the single-sample diploid case. | ||
| */ | ||
| @Advanced | ||
| @Argument(fullName = "input-prior", doc = "Input prior for calls", optional = true) |
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Oh thank goodness this is gone.
| @@ -154,6 +155,30 @@ public AFCalculationResult calculate(final VariantContext vc, final int defaultP | |||
| return new AFCalculationResult(integerAltAlleleCounts, alleles, log10PNoVariant, log10PRefByAllele); | |||
| } | |||
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| /** | |||
| * Calculate the posterior probability that a single biallelic sample is non-ref | |||
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I don't like the phrase biallelic sample, but I get that the gist is single-sample. Maybe biallelic genotype?
| @@ -292,6 +293,36 @@ public void testSpanningDeletionWithVeryUnlikelyAltAllele() { | |||
| final double log10PVariant = afCalc.calculate(vc).log10ProbVariantPresent(); | |||
| } | |||
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| //check the exact integration calculation | |||
| @Test | |||
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Lovely tests, as always.
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Closes #6111.
The qual used in HC's
isActivemethod now matches that ofGenotypeGVCFs. That is, they both now use the new qual. This lets us finally deleteAFPriorProvider. I have profiled and HaplotypeCaller speeds up in this branch by a negligible but measurable amount.@ldgauthier Can you look at this? the big paragraph changed in the new qual notes is just correcting the omission of some
-1s and has nothing to do with the single-sample calculation.