From 8bdf49a01f82992e834e04a07615b525257e9488 Mon Sep 17 00:00:00 2001 From: depristo Date: Wed, 25 Mar 2009 03:12:54 +0000 Subject: [PATCH] added slightly more useful output to Depth of Coverage walker. (now prints number of loci). Traversal engine now actually prints the reduce result (key) and no longer prints millions of locus interval updates git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@183 348d0f76-0448-11de-a6fe-93d51630548a --- java/src/org/broadinstitute/sting/gatk/TraversalEngine.java | 4 ++-- .../sting/gatk/walkers/DepthOfCoverageWalker.java | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) 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; }