diff --git a/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java index 76875393e..2f90eef0d 100755 --- a/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java @@ -339,7 +339,7 @@ public class TraversalEngine { */ protected void printOnTraversalDone(final String type, T sum) { printProgress(true, type, null); - logger.info(String.format("Traversal reduce result is " + sum)); + System.out.printf(String.format("Traversal reduce result is %d%n", sum)); // TODO: fixme -- how do we use this logger? logger.info(String.format("Traversal skipped %d reads out of %d total (%.2f%%)", nSkippedReads, nReads, (nSkippedReads * 100.0) / nReads)); logger.info(String.format(" -> %d unmapped reads", nUnmappedReads)); logger.info(String.format(" -> %d non-primary reads", nNotPrimary)); @@ -652,7 +652,7 @@ public class TraversalEngine { samReader = initializeSAMFile(readsFile); for ( GenomeLoc interval : locs ) { - System.out.printf("Processing locus %s%n", interval.toString()); + logger.debug(String.format("Processing locus %s", interval.toString())); CloseableIterator readIter = samReader.queryOverlapping( interval.getContig(), (int)interval.getStart(), diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java index 1253f245c..5c75b5443 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java @@ -15,7 +15,7 @@ import java.util.List; public class DepthOfCoverageWalker extends BasicLociWalker { public Integer map(List rodData, char ref, LocusContext context) { System.out.printf("%s: %d%n", context.getLocation(), context.getReads().size() ); - return 0; + return 1; } public Integer reduceInit() { return 0; }