Examples of org.broadinstitute.gatk.utils.SimpleTimer.start()

Class org.broadinstitute.gatk.utils.SimpleTimer

Examples of org.broadinstitute.gatk.utils.SimpleTimer.start()

org.broadinstitute.gatk.utils.SimpleTimer.start()
Starts the timer running, and sets the elapsedTimeNano time to 0. This is equivalent to resetting the time to have no history at all. @return this object, for programming convenience

                final double[] priors = testBuilder.makePriors();


                for ( int[] ACs : makeACs(testBuilder.numAltAlleles, testBuilder.nSamples*2) ) {
                    final VariantContext vc = testBuilder.makeACTest(ACs, 0, nonTypePL);


                    timer.start();
                    final AFCalculationResult resultTracker = calc.getLog10PNonRef(vc, HomoSapiensConstants.DEFAULT_PLOIDY, testBuilder.numAltAlleles, priors);
                    final long runtime = timer.getElapsedTimeNano();


                    int otherAC = 0;
                    int nAltSeg = 0;

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                    final VariantContextBuilder vcb = new VariantContextBuilder(vc);
                    final List<Genotype> genotypes = new ArrayList<Genotype>(vc.getGenotypes());
                    Collections.rotate(genotypes, position);
                    vcb.genotypes(genotypes);


                    timer.start();
                    final AFCalculationResult resultTracker = calc.getLog10PNonRef(vcb.make(), HomoSapiensConstants.DEFAULT_PLOIDY, testBuilder.numAltAlleles, priors);
                    final long runtime = timer.getElapsedTimeNano();


                    final List<Object> columns = new LinkedList<Object>(coreValues);
                    columns.addAll(Arrays.asList(runtime, resultTracker.getnEvaluations(), nonTypePL, position));

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                ac[0] = 1;


                for ( int nNonInformative = 0; nNonInformative < testBuilder.nSamples; nNonInformative++ ) {
                    final VariantContext vc = testBuilder.makeACTest(ac, nNonInformative, nonTypePL);


                    timer.start();
                    final AFCalculationResult resultTracker = calc.getLog10PNonRef(vc, HomoSapiensConstants.DEFAULT_PLOIDY, testBuilder.numAltAlleles, priors);
                    final long runtime = timer.getElapsedTimeNano();


                    final List<Object> columns = new LinkedList<Object>(coreValues);
                    columns.addAll(Arrays.asList(runtime, resultTracker.getnEvaluations(), nonTypePL, nNonInformative));

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