move elseif

broadinstitute · May 10, 2022 · 2152ad8 · 2152ad8
1 parent b777040
commit 2152ad8
Showing 1 changed file with 12 additions and 13 deletions.
diff --git a/.../org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java b/.../org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java
@@ -538,24 +538,23 @@ private GenotypesContext mergeRefConfidenceGenotypes(final VariantContext vc,
             final int ploidy = g.getPloidy();
             final GenotypeBuilder genotypeBuilder = new GenotypeBuilder(g);
             if (!doSomaticMerge) {
-                if (g.hasPL() | g.hasAD()) {
+                if (g.hasPL()) {
+                    // lazy initialization of the genotype index map by ploidy.
                     int[]  perSampleIndexesOfRelevantAlleles = AlleleSubsettingUtils.getIndexesOfRelevantAllelesForGVCF(remappedAlleles, targetAlleles, vc.getStart(), g, false);
-                    if (g.hasPL()) {
-                        // lazy initialization of the genotype index map by ploidy.
-                        final int[] genotypeIndexMapByPloidy = genotypeIndexMapsByPloidy[ploidy] == null
-                                ? calculators.getInstance(ploidy, maximumAlleleCount).genotypeIndexMap(perSampleIndexesOfRelevantAlleles, calculators) //probably horribly slow
-                                : genotypeIndexMapsByPloidy[ploidy];
-                        final int[] PLs = generatePL(g, genotypeIndexMapByPloidy);
-                        genotypeBuilder.PL(PLs);
-                    }
-                    if (g.hasAD()) {
-                        final int[] AD = g.hasAD() ? AlleleSubsettingUtils.generateAD(g.getAD(), perSampleIndexesOfRelevantAlleles) : null;
-                        genotypeBuilder.AD(AD);
-                    }
+                    final int[] genotypeIndexMapByPloidy = genotypeIndexMapsByPloidy[ploidy] == null
+                            ? calculators.getInstance(ploidy, maximumAlleleCount).genotypeIndexMap(perSampleIndexesOfRelevantAlleles, calculators) //probably horribly slow
+                            : genotypeIndexMapsByPloidy[ploidy];
+                    final int[] PLs = generatePL(g, genotypeIndexMapByPloidy);
+                    genotypeBuilder.PL(PLs);
                 // clean up low confidence hom refs for better annotations later
                 } else if (GenotypeGVCFsEngine.excludeFromAnnotations(g)) {
                     genotypeBuilder.alleles(Collections.nCopies(ploidy, Allele.NO_CALL));
                 }
+                if (g.hasAD()) {
+                    int[]  perSampleIndexesOfRelevantAlleles = AlleleSubsettingUtils.getIndexesOfRelevantAllelesForGVCF(remappedAlleles, targetAlleles, vc.getStart(), g, false);
+                    final int[] AD = g.hasAD() ? AlleleSubsettingUtils.generateAD(g.getAD(), perSampleIndexesOfRelevantAlleles) : null;
+                    genotypeBuilder.AD(AD);
+                }
             }
             else {  // doSomaticMerge
                 genotypeBuilder.noAttributes();