diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java index 522cfcb17..5636db94f 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java @@ -25,7 +25,7 @@ import edu.mit.broad.picard.util.OverlapDetector; import edu.mit.broad.picard.directed.IntervalList; @By(DataSource.REFERENCE) -public class HybSelPerformanceWalker extends LocusWalker { +public class HybSelPerformanceWalker extends LocusWalker implements TreeReducible { @Argument(fullName="min_mapq", shortName="mmq", required=false, doc="Minimum mapping quality of reads to consider") public Integer MIN_MAPQ = 1; @@ -123,6 +123,10 @@ public class HybSelPerformanceWalker extends LocusWalker bait_quant_hits = bait_quant.getOverlaps(targetInterval); String bait_quant_string = (bait_quant_hits.size() == 1) ? bait_quant_hits.iterator().next().getName() : "0"; - if (bait_quant_hits.size() <= 1) { out.printf("Warning: multiple bait quantity intervals detected; perhaps bait quantity interval lengths don't match primary interval list specified with -L"); } + if (bait_quant_hits.size() > 1) { out.printf("Warning: multiple bait quantity intervals detected; perhaps bait quantity interval lengths don't match primary interval list specified with -L\n"); } int adjacent_baits = adjacent_bait_detector.getOverlaps(targetInterval).size() - 1; out.printf("%s:%d-%d\t%d\t%6.4f\t%6.4f\t%6.4f\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%s\t%s\t%d\n",