check for is empty

broadinstitute · Mar 19, 2021 · a4f8290 · a4f8290
1 parent e389981
commit a4f8290
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/ShiftFasta.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/ShiftFasta.java
@@ -113,7 +113,7 @@ public void traverse() {
             throw new UserException.BadInput("Reference length is too long");
         }
         List<SAMSequenceRecord> contigs = refSource.getSequenceDictionary().getSequences();
-        final ListIterator<Integer> shiftOffsetsIt = (shiftOffsets != null && shiftOffsets.size() == contigs.size()) ?
+        final ListIterator<Integer> shiftOffsetsIt = (shiftOffsets != null && !shiftOffsets.isEmpty() && shiftOffsets.size() == contigs.size()) ?
                 shiftOffsets.listIterator() : null;
         refSource.getSequenceDictionary().getSequences().forEach(seq -> shiftContig(seq, shiftOffsetsIt));
     }