Package org.bioinfo.ngs.qc.qualimap.process

Examples of org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis.run()

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            BamQCRegionReporter bamQcReporter = new BamQCRegionReporter(false, true);


            try {
                bamQc.run();
                bamQcReporter.loadReportData(bamQc.getBamStats());
                bamQcReporter.computeChartsBuffers(bamQc.getBamStats(), bamQc.getLocator(), bamQc.isPairedData());
            } catch (Exception e) {
                assertTrue("Error calculating stats. " + e.getMessage(), false);
                e.printStackTrace();
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        bamDialog.setUiEnabled(false);
        bamDialog.getProgressStream().setText("Running BAM file analysis...");

    try {

            bamQC.run();
          //timer.cancel();

      bamDialog.getProgressStream().setText("End of bam qc");
            bamDialog.getProgressBar().setValue(100);
 
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        bamQC.setNumberOfReadsInBunch(bunchSize);
        bamQC.setProtocol(protocol);
        bamQC.setMinHomopolymerSize(minHomopolymerSize);

    // run evaluation
    bamQC.run();

    logger.println("end of bam qc");

    logger.println("Computing report...");
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