From d31c658c2ec13e111d0607fe3cbe9ff7ebd72a2e Mon Sep 17 00:00:00 2001 From: depristo Date: Mon, 3 Jan 2011 02:09:08 +0000 Subject: [PATCH] Organized performance monitoring passes unit tests and is more efficient git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4924 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/traversals/TraversalEngine.java | 21 ++++++++----------- 1 file changed, 9 insertions(+), 12 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java index 6e35a398c..ec6e93aae 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java @@ -127,18 +127,6 @@ public abstract class TraversalEngine,Provide // // code to process the performance log // - // TODO -- should be controlled by Queue so that .out and .performance.log comes out - // - if ( PERFORMANCE_LOG_ENABLED && performanceLog == null - && engine != null && engine.getArguments().performanceLog != null ) { - try { - performanceLog = new PrintStream(new FileOutputStream(engine.getArguments().performanceLog)); - performanceLog.println(Utils.join("\t", Arrays.asList("elapsed.time", "units.processed", "processing.speed"))); - } catch (FileNotFoundException e) { - throw new UserException.CouldNotCreateOutputFile(engine.getArguments().performanceLog, e); - } - } - if ( performanceLog != null && maxElapsedIntervalForPrinting(curTime, lastPerformanceLogPrintTime, PERFORMANCE_LOG_PRINT_FREQUENCY)) { lastPerformanceLogPrintTime = curTime; if ( nRecords > 1 ) performanceLog.printf("%.2f\t%d\t%.2f%n", elapsed, nRecords, secsPer1MReads); @@ -180,6 +168,15 @@ public abstract class TraversalEngine,Provide */ public void initialize(GenomeAnalysisEngine engine) { this.engine = engine; + + if ( PERFORMANCE_LOG_ENABLED && engine != null && engine.getArguments() != null && engine.getArguments().performanceLog != null ) { + try { + performanceLog = new PrintStream(new FileOutputStream(engine.getArguments().performanceLog)); + performanceLog.println(Utils.join("\t", Arrays.asList("elapsed.time", "units.processed", "processing.speed"))); + } catch (FileNotFoundException e) { + throw new UserException.CouldNotCreateOutputFile(engine.getArguments().performanceLog, e); + } + } } /**