From 3a6b4b43b78d6888d785e88c6e1b87f1da58cc75 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sun, 13 Jan 2013 09:53:10 -0500
Subject: [PATCH] Backporting LIBSPerformance improvements to original commit

---
 .../sting/utils/locusiterator/LIBSPerformance.java  | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/locusiterator/LIBSPerformance.java b/public/java/src/org/broadinstitute/sting/utils/locusiterator/LIBSPerformance.java
index 82d589ff8..0985ed196 100644
--- a/public/java/src/org/broadinstitute/sting/utils/locusiterator/LIBSPerformance.java
+++ b/public/java/src/org/broadinstitute/sting/utils/locusiterator/LIBSPerformance.java
@@ -37,10 +37,7 @@ import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.iterators.GATKSAMIterator;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@@ -100,12 +97,18 @@ public class LIBSPerformance extends CommandLineProgram {
                         samples,
                         false);
 
+        final SimpleTimer timer = new SimpleTimer().start();
         int bp = 0;
+        double lastElapsed = 0;
         while ( libs.hasNext() ) {
             AlignmentContext context = libs.next();
-            if ( ++bp % 100000 == 0 )
+            bp++;
+            if ( timer.getElapsedTime() - lastElapsed > 10 ) {
                 logger.info(bp + " iterations at " + context.getLocation());
+                lastElapsed = timer.getElapsedTime();
+            }
         }
+        logger.info(String.format("runtime in seconds: %.2f", timer.getElapsedTime()));
 
         return 0;
     }