From 2152ad8754b2e276e8104e05f1d9639ac5397271 Mon Sep 17 00:00:00 2001
From: Rori Cremer <6863459+RoriCremer@users.noreply.github.com>
Date: Fri, 6 May 2022 09:27:49 -0400
Subject: [PATCH] move elseif

---
 ...ferenceConfidenceVariantContextMerger.java | 25 +++++++++----------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java
index badf09b785d..6e8c27aba84 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java
+++ b/src/main/java/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();