diff --git a/playground/java/src/org/broadinstitute/sting/indels/IndelInspector.java b/playground/java/src/org/broadinstitute/sting/indels/IndelInspector.java index fdf50c55e..7b16b94bb 100755 --- a/playground/java/src/org/broadinstitute/sting/indels/IndelInspector.java +++ b/playground/java/src/org/broadinstitute/sting/indels/IndelInspector.java @@ -250,7 +250,7 @@ public class IndelInspector extends CommandLineProgram { setDefaultContigOrdering(); return; } - List seqs = h.getSequences(); + List seqs = h.getSequenceDictionary().getSequences(); if ( seqs == null ) { System.out.println("No reference sequence records found in SAM file header, " + "falling back to default contig ordering");