fix(namedAlleleMatcher): don't print duplication warnings for cases d…

…ealt by preprocessor
PharmGKB · Feb 28, 2025 · 5ff5649 · 5ff5649
1 parent 2b8815b
commit 5ff5649
Showing 1 changed file with 8 additions and 2 deletions.
diff --git a/src/main/java/org/pharmgkb/pharmcat/haplotype/VcfReader.java b/src/main/java/org/pharmgkb/pharmcat/haplotype/VcfReader.java
@@ -256,8 +256,14 @@ public void parseLine(VcfMetadata metadata, VcfPosition position, List<VcfSample
 
     final String chrPos = position.getChromosome() + ":" + position.getPosition();
     if (m_alleleMap.containsKey(chrPos)) {
-      addWarning(chrPos, "Duplicate entry found in VCF; this entry trumps others.",
-          "Duplicate entry: first valid position wins");
+      // The preprocessor will split out PGx variants and non-PGx variants into 2 separate lines and add a filter code
+      // on the second entry. Don't bother printing warning in this case.
+      if (!position.getFilters().contains(sf_filterCodeRef) &&
+          !position.getFilters().contains(sf_filterCodeAlt) &&
+          !position.getFilters().contains(sf_filterCodeIndel)) {
+        addWarning(chrPos, "Duplicate entry found in VCF; first valid entry trumps others.",
+            "Duplicate entry: first valid position wins");
+      }
       return;
     }