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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
This commit is contained in:
depristo 2010-10-26 20:22:16 +00:00
parent b085648141
commit e02aac0743
1 changed files with 5 additions and 4 deletions
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9
java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
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@ -123,10 +123,11 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
nSkippedReads += countsByFilter.getValue(); nSkippedReads += countsByFilter.getValue();
logger.info(String.format("Total runtime %.2f secs, %.2f min, %.2f hours", elapsed, elapsed / 60, elapsed / 3600)); 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%%)", if ( cumulativeMetrics.getNumReadsSeen() > 0 )
nSkippedReads, logger.info(String.format("%d reads were filtered out during traversal out of %d total (%.2f%%)",
cumulativeMetrics.getNumReadsSeen(), nSkippedReads,
100.0 * MathUtils.ratio(nSkippedReads,cumulativeMetrics.getNumReadsSeen()))); cumulativeMetrics.getNumReadsSeen(),
100.0 * MathUtils.ratio(nSkippedReads,cumulativeMetrics.getNumReadsSeen())));
for ( Map.Entry<Class, Long> filterCounts : cumulativeMetrics.getCountsByFilter().entrySet() ) { for ( Map.Entry<Class, Long> filterCounts : cumulativeMetrics.getCountsByFilter().entrySet() ) {
long count = filterCounts.getValue(); long count = filterCounts.getValue();
logger.info(String.format(" -> %d reads (%.2f%% of total) failing %s", logger.info(String.format(" -> %d reads (%.2f%% of total) failing %s",