Fix ReblockGVCF NPE on no-calls #5863
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ldgauthier
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@@ Coverage Diff @@
## master #5863 +/- ##
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- Coverage 86.841% 13.378% -73.464%
+ Complexity 32327 6386 -25941
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Files 1991 2011 +20
Lines 149347 151036 +1689
Branches 16482 16151 -331
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- Hits 129695 20205 -109490
- Misses 13646 128567 +114921
+ Partials 6006 2264 -3742
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droazen
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Apr 8, 2019
| return Collections.emptyMap(); | ||
| } | ||
| final Pair<Integer, Double> sampleCountCoeff = calculateIC(vc, genotypes); | ||
| final int sampleCount = sampleCountCoeff.getLeft(); | ||
| final double F = sampleCountCoeff.getRight(); | ||
| if (sampleCount < MIN_SAMPLES) { | ||
| logger.warn("Annotation will not be calculated, must provide at least " + MIN_SAMPLES + " samples"); | ||
| logger.warn("InbreedingCoeff will not be calculated for at least one position; at least " + MIN_SAMPLES + " samples must have called genotypes"); |
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Did you want separate "one shot" loggers for these 2 warnings? (ie., would you ever want both warnings to be emitted?)
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The first one is like "hey, you don't have enough samples in your cohort" and the second one is like "oops, there are a lot of no-calls at this site, so I'm not going to output a value here", so they should be mutually exclusive.
| final Genotype g2 = makeG("sample1", Allele.NO_CALL,Allele.NO_CALL); | ||
| final VariantContext noData = makeDeletionVC("noData", Arrays.asList(LONG_REF, DELETION, Allele.NON_REF_ALLELE), LONG_REF.length(), g2); | ||
| final VariantContext notCrashing = reblocker.lowQualVariantToGQ0HomRef(noData, noData); | ||
| Assert.assertTrue(notCrashing.getGenotype(0).isNoCall()); |
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Add a comment explaining this test case (ie., explain what the "crash" being tested for was)
| final Genotype g2 = makeG("sample1", Allele.NO_CALL,Allele.NO_CALL); | ||
| final VariantContext noData = makeDeletionVC("noData", Arrays.asList(LONG_REF, DELETION, Allele.NON_REF_ALLELE), LONG_REF.length(), g2); | ||
| final VariantContext notCrashing = reblocker.lowQualVariantToGQ0HomRef(noData, noData); | ||
| Assert.assertTrue(notCrashing.getGenotype(0).isNoCall()); | ||
| } | ||
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| @Test |
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Can you add a test case covering the change to shouldBeReblocked() as well (and make that method @VisibleForTesting?)
Copy AS annotations too Put RAW_MQandDP back to int tuple so GDB doesn't duck it up Fix MQ bug, upgrade from experimental to beta
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@droazen I addressed your comments, but I also added some more fixes (and tests!) |
MIN_DP, floor GQs for each block
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Closing this one -- these changes to |
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