Fix genotype allele remapping issue

broadinstitute · Jun 24, 2019 · 9539a42 · 9539a42
1 parent 746c7b5
commit 9539a42
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/evoquer/Evoquer.java b/src/main/java/org/broadinstitute/hellbender/tools/evoquer/Evoquer.java
@@ -99,7 +99,7 @@ public class Evoquer extends GATKTool {
             fullName = "run-query-only",
             doc = "If true, just do the query against BigQuery and retrieve the resulting records, but don't write a VCF",
             optional = true)
-    private boolean runQueryOnly = true;
+    private boolean runQueryOnly = false;
 
     @Argument(
             fullName = "disable-gnarly-genotyper",

diff --git a/.../org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java b/.../org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java
@@ -536,14 +536,18 @@ private GenotypesContext mergeRefConfidenceGenotypes(final VariantContext vc,
             if (!doSomaticMerge) {
                 if (g.hasPL()) {
                     // lazy initialization of the genotype index map by ploidy.
-                    int[]  perSampleIndexesOfRelevantAlleles = getIndexesOfRelevantAlleles(remappedAlleles, targetAlleles, vc.getStart(), g);
+                    int[] perSampleIndexesOfRelevantAlleles = getIndexesOfRelevantAlleles(remappedAlleles, targetAlleles, vc.getStart(), g);
                     final int[] genotypeIndexMapByPloidy = genotypeIndexMapsByPloidy[ploidy] == null
                             ? calculators.getInstance(ploidy, maximumAlleleCount).genotypeIndexMap(perSampleIndexesOfRelevantAlleles, calculators) //probably horribly slow
                             : genotypeIndexMapsByPloidy[ploidy];
                     final int[] PLs = generatePL(g, genotypeIndexMapByPloidy);
                     final int[] AD = g.hasAD() ? generateAD(g.getAD(), perSampleIndexesOfRelevantAlleles) : null;
                     genotypeBuilder.PL(PLs).AD(AD);
                 }
+
+                final List<Allele> remappedGTAlleles = g.getAlleles().stream().map(a -> (vc.getAlleleIndex(a) > -1 ? remappedAlleles.get(vc.getAlleleIndex(a)) : Allele.NO_CALL)).collect(Collectors.toList());
+                genotypeBuilder.alleles(remappedGTAlleles);
+                genotypeBuilder.name(name);
             }
             else {
                 genotypeBuilder.noAttributes();