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

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

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            bamDialog.getProgressBar().setValue(100);
 
      // report
      bamDialog.getProgressStream().setText("Computing report...");
      BamQCRegionReporter reporter = new BamQCRegionReporter(regionsAvailable, true);
            bamQC.prepareInputDescription(reporter, bamDialog.getDrawChromosomeLimits());

      // Draw the Chromosome Limits or not
      reporter.setPaintChromosomeLimits( bamDialog.getDrawChromosomeLimits() );
            if (bamDialog.compareGcContentToPrecalculated()) {
                String genomeName = bamDialog.getGenomeName();
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            if (bamDialog.getRegionFile() != null && bamDialog.getComputeOutsideRegions() ) {

                BamQCRegionReporter outsideReporter = new BamQCRegionReporter(regionsAvailable, false);

                bamQC.prepareInputDescription(outsideReporter, bamDialog.getDrawChromosomeLimits());
              // Draw the Chromosome Limits or not
        outsideReporter.setPaintChromosomeLimits(bamDialog.getDrawChromosomeLimits());

                if (bamDialog.compareGcContentToPrecalculated()) {
                    String genomeName = bamDialog.getGenomeName();
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    reporter.setPaintChromosomeLimits(paintChromosomeLimits);
        if (!genomeToCompare.isEmpty()) {
            reporter.setGenomeGCContentName(genomeToCompare);
        }

        bamQC.prepareInputDescription(reporter, paintChromosomeLimits);

    // save stats

        reporter.writeReport(bamQC.getBamStats(),outdir);
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            BamQCRegionReporter outsideReporter = new BamQCRegionReporter(selectedRegionsAvailable, false);
            outsideReporter.setPaintChromosomeLimits(paintChromosomeLimits);
            if (!genomeToCompare.isEmpty()) {
                outsideReporter.setGenomeGCContentName(genomeToCompare);
            }
            bamQC.prepareInputDescription(outsideReporter, paintChromosomeLimits);
            outsideReporter.writeReport(bamQC.getOutsideBamStats(),outdir);

            outsideReporter.loadReportData(bamQC.getOutsideBamStats());
            outsideReporter.computeChartsBuffers(bamQC.getOutsideBamStats(), bamQC.getLocator(), bamQC.isPairedData());
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