Change CleanSam to use getReferencePath.

broadinstitute · May 3, 2022 · 4a099f5 · 4a099f5
1 parent abf2c67
commit 4a099f5
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/src/main/java/picard/sam/CleanSam.java b/src/main/java/picard/sam/CleanSam.java
@@ -71,7 +71,7 @@ public class CleanSam extends CommandLineProgram {
     protected int doWork() {
         IOUtil.assertFileIsReadable(INPUT);
         IOUtil.assertFileIsWritable(OUTPUT);
-        final SamReaderFactory factory = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE);
+        final SamReaderFactory factory = SamReaderFactory.makeDefault().referenceSequence(referenceSequence.getReferencePath());
         if (VALIDATION_STRINGENCY == ValidationStringency.STRICT) {
             factory.validationStringency(ValidationStringency.LENIENT);
         }