From e02aac07439a1e2e565fd235255afa28df36acdb Mon Sep 17 00:00:00 2001 From: depristo Date: Tue, 26 Oct 2010 20:22:16 +0000 Subject: [PATCH] No longer print out 0 reads were filtered out... message when there were no reads scene at all git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4575 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/traversals/TraversalEngine.java | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java index ea1e6d4fe..d28911d11 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java @@ -123,10 +123,11 @@ public abstract class TraversalEngine,Provide nSkippedReads += countsByFilter.getValue(); logger.info(String.format("Total runtime %.2f secs, %.2f min, %.2f hours", elapsed, elapsed / 60, elapsed / 3600)); - logger.info(String.format("%d reads were filtered out during traversal out of %d total (%.2f%%)", - nSkippedReads, - cumulativeMetrics.getNumReadsSeen(), - 100.0 * MathUtils.ratio(nSkippedReads,cumulativeMetrics.getNumReadsSeen()))); + if ( cumulativeMetrics.getNumReadsSeen() > 0 ) + logger.info(String.format("%d reads were filtered out during traversal out of %d total (%.2f%%)", + nSkippedReads, + cumulativeMetrics.getNumReadsSeen(), + 100.0 * MathUtils.ratio(nSkippedReads,cumulativeMetrics.getNumReadsSeen()))); for ( Map.Entry filterCounts : cumulativeMetrics.getCountsByFilter().entrySet() ) { long count = filterCounts.getValue(); logger.info(String.format(" -> %d reads (%.2f%% of total) failing %s",