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

Class org.broadinstitute.gatk.utils.SimpleTimer

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

org.broadinstitute.gatk.utils.SimpleTimer.currentTime()
@return A convenience function to obtain the current time in milliseconds from this timer

            final SimpleTimer timer = new SimpleTimer().start();


            if ( totalNumberOfFiles > 0 ) logger.info("Initializing SAMRecords in serial");
            final int tickSize = 50;
            int nExecutedTotal = 0;
            long lastTick = timer.currentTime();
            for(final SAMReaderID readerID: readerIDs) {
                final ReaderInitializer init = new ReaderInitializer(readerID).call();


                checkForUnsupportedBamFile(init.reader.getFileHeader());

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                }


                logger.debug(String.format("Processing file (%d of %d) %s...", readerNumber++, totalNumberOfFiles,  readerID.samFile));
                readers.put(init.readerID,init.reader);
                if ( ++nExecutedTotal % tickSize == 0) {
                    double tickInSec = (timer.currentTime() - lastTick) / 1000.0;
                    printReaderPerformance(nExecutedTotal, tickSize, totalNumberOfFiles, timer, tickInSec);
                    lastTick = timer.currentTime();
                }
            }

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                logger.debug(String.format("Processing file (%d of %d) %s...", readerNumber++, totalNumberOfFiles,  readerID.samFile));
                readers.put(init.readerID,init.reader);
                if ( ++nExecutedTotal % tickSize == 0) {
                    double tickInSec = (timer.currentTime() - lastTick) / 1000.0;
                    printReaderPerformance(nExecutedTotal, tickSize, totalNumberOfFiles, timer, tickInSec);
                    lastTick = timer.currentTime();
                }
            }


            if ( totalNumberOfFiles > 0 ) logger.info(String.format("Done initializing BAM readers: total time %.2f", timer.getElapsedTime()));

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