Examples of org.bioinfo.ngs.qc.qualimap.beans.BamStats

    }


    private void propagateRead(char[] alignment,long readStart, long readEnd,
                               int mappingQuality ){
        // init covering stat
        BamStats bamStats = ctx.getBamStats();
    int index = bamStats.getNumberOfProcessedWindows()+1;


    BamGenomeWindow adjacentWindow;
    boolean outOfBounds = true;
    while(outOfBounds && index < bamStats.getNumberOfWindows()){


      // next currentWindow
      long ws = bamStats.getWindowStart(index);


        synchronized (lock) {
                ConcurrentMap<Long,BamGenomeWindow> openWindows = ctx.getOpenWindows();
                adjacentWindow = ctx.getOpenWindow(ws, bamStats, openWindows);
                if (computeOutsideStats) {

        // init window set
        windowSize = computeWindowSize(referenceSize,numberOfWindows);
        //effectiveNumberOfWindows = computeEffectiveNumberOfWindows(referenceSize,windowSize);
        List<Long> windowPositions = computeWindowPositions(windowSize);
        effectiveNumberOfWindows = windowPositions.size();
        bamStats = new BamStats("genome", locator, referenceSize,effectiveNumberOfWindows);
        logger.println("Number of windows: " + numberOfWindows +
                ", effective number of windows: " + effectiveNumberOfWindows);
        logger.println("Chunk of reads size: " + numReadsInBunch);
        logger.println("Number of threads: " + threadNumber);
        bamStats.setSourceFile(bamFile);
        //bamStats.setWindowReferences("w",windowSize);
        bamStats.setWindowReferences("w", windowPositions);
        bamStatsCollector = new BamStatsCollector();
        openWindows = new ConcurrentHashMap<Long,BamGenomeWindow>();


        if (saveCoverage) {
            bamStats.activateCoverageReporting(pathToCoverageReport, nonZeroCoverageOnly);
        }


        //regions
        if(selectedRegionsAvailable){


      // load selected regions
            loadSelectedRegions();
            outsideBamStatsCollector = new BamStatsCollector();


            // outside of regions stats
            if (computeOutsideStats) {
                outsideBamStats = new BamStats("outside", locator, referenceSize, effectiveNumberOfWindows);
                outsideBamStats.setSourceFile(bamFile);
                outsideBamStats.setWindowReferences("out_w", windowPositions);
                openOutsideWindows = new HashMap<Long,BamGenomeWindow>();
                currentOutsideWindow = nextWindow(outsideBamStats,openOutsideWindows,reference,true);

Examples of org.bioinfo.ngs.qc.qualimap.beans.BamStats

Related Classes of org.bioinfo.ngs.qc.qualimap.beans.BamStats