From 1945712d3f0ac117c0e432a3bb3d2f0b6f1ee23e Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Wed, 21 Jun 2023 16:49:36 -0700
Subject: [PATCH] Allow SampleSpecificGenotypeFiltration to run when the filter
 expression arguments dont match sample sets (#248)

---
 .../discvrseq/walkers/SampleSpecificGenotypeFiltration.java    | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/main/java/com/github/discvrseq/walkers/SampleSpecificGenotypeFiltration.java b/src/main/java/com/github/discvrseq/walkers/SampleSpecificGenotypeFiltration.java
index b16c4f80..f86c98e4 100644
--- 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);