Add haploid support to GnarlyGenotyper #7750
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meganshand
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Jul 12, 2023
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| for ( final Genotype g : vc.getGenotypes() ) { | ||
| final String name = g.getSampleName(); | ||
| if(g.getPloidy() != ASSUMED_PLOIDY && !isGDBnoCall(g)) { | ||
| /*if(g.getPloidy() != ASSUMED_PLOIDY && !isGDBnoCall(g)) { |
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can delete this commented out section
| /** | ||
| * Some legacy versions of GenomicsDB report no-calls as `0` or `.` | ||
| * @param g genotype to check | ||
| * @return true if this is a genotype that should be represented as a ploidy-aware, spec compliant no-call | ||
| */ | ||
| private static boolean isGDBnoCall(final Genotype g) { | ||
| return g.getPloidy() == 1 && (g.getAllele(0).isReference() || g.getAllele(0).isNoCall()); | ||
| //return g.getPloidy() == 1 && (g.getAllele(0).isReference() || g.getAllele(0).isNoCall()); |
| gb.attribute(GATKVCFConstants.GENOTYPE_QUALITY_BY_ALT_CONFIDENCE, ALTGQ); | ||
| gb.noPL(); | ||
| } | ||
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| /** | ||
| * Some legacy versions of GenomicsDB report no-calls as `0` or `.` | ||
| * @param g genotype to check | ||
| * @return true if this is a genotype that should be represented as a ploidy-aware, spec compliant no-call |
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I think you can update this comment since it's no longer checking the ploidy
| @@ -1,5 +1,8 @@ | |||
| package org.broadinstitute.hellbender.tools.walkers; | |||
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| import com.google.errorprone.annotations.Var; | |||
| @@ -217,4 +224,26 @@ public void testOnEmptyAnnotations() { | |||
| Assert.assertEquals(sors.get(1), VCFConstants.MISSING_VALUE_v4); | |||
| } | |||
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| @Test | |||
| public void testHaploidInput() { | |||
| final File haploidGVCF = new File(getToolTestDataDir(), "haploid.mini.g.vcf"); | |||
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I think haploid.mini.g.vcf is missing
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Github actions tests reported job failures from actions build 5533855739
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meganshand
approved these changes
Jul 17, 2023
| @@ -53,13 +53,19 @@ public void assertThatExpectedOutputUpdateToggleIsDisabled() { | |||
| @DataProvider(name="VCFdata") | |||
| public Object[][] getVCFdata() { | |||
| return new Object[][]{ | |||
| /* | |||
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Addresses #7690