Allow SampleSpecificGenotypeFiltration to run when the filter express…

…ion arguments dont match sample sets (#248)
BimberLab · Jun 21, 2023 · 1945712 · 1945712
1 parent 7f69944
commit 1945712
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/src/main/java/com/github/discvrseq/walkers/SampleSpecificGenotypeFiltration.java b/src/main/java/com/github/discvrseq/walkers/SampleSpecificGenotypeFiltration.java
@@ -96,7 +96,8 @@ public void onTraversalStart() {
             String genotypeExpr = StringUtils.join(Arrays.copyOfRange(tokens, 1, tokens.length));
 
             if (!allSetNames.contains(setName)) {
-                throw new GATKException("Unknown set name for filter: " + expr);
+                logger.warn("Unknown set name for filter, skipping: " + expr);
+                continue;
             }
 
             Pair<List<String>, List<String>> filters = setToFilterStrings.get(setName);