Package org.bioinfo.ngs.qc.qualimap.beans

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

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                               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);
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        // wait till all tasks are finished
        for (Future<ProcessBunchOfReadsTask.Result> result : results) {
            ProcessBunchOfReadsTask.Result taskResult = result.get();
            Collection<SingleReadData> dataset = taskResult.getReadAlignmentData();
            for (SingleReadData rd : dataset) {
                BamGenomeWindow w = openWindows.get(rd.getWindowStart());
                w.addReadAlignmentData(rd);
            }
            bamStats.addReadStatsData( taskResult.getReadStatsCollector() );

            if (selectedRegionsAvailable && computeOutsideStats) {
                Collection<SingleReadData> outsideData = taskResult.getOutOfRegionReadsData();
                for (SingleReadData rd : outsideData) {
                    BamGenomeWindow w = openOutsideWindows.get( rd.getWindowStart() );
                    w.addReadAlignmentData(rd);
                }
                outsideBamStats.addReadStatsData( taskResult.getOutRegionReadStatsCollector() );

            }
        }
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    }


    public BamGenomeWindow getOpenWindow(long windowStart,BamStats bamStats,
                                         Map<Long,BamGenomeWindow> openWindows) {
        BamGenomeWindow window;
        if(openWindows.containsKey(windowStart)){
            window = openWindows.get(windowStart);
        } else {
            int numInitWindows = bamStats.getNumberOfInitializedWindows();
            String windowName = bamStats.getWindowName(numInitWindows);
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        byte[]miniReference = null;
    if(reference != null) {
      miniReference = Arrays.copyOfRange(reference, (int) (windowStart - 1), (int) (windowEnd - 1));
    }

        BamGenomeWindow w = detailed ? new BamDetailedGenomeWindow(name,windowStart,windowEnd,miniReference) :
                    new BamGenomeWindow(name,windowStart,windowEnd,miniReference);

        if (selectedRegionsAvailable) {
            calculateRegionsLookUpTableForWindow(w);
        }
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  }


    private BamGenomeWindow nextWindow(BamStats bamStats, Map<Long,BamGenomeWindow> openWindows,byte[]reference,boolean detailed){
    // init new current
    BamGenomeWindow currentWindow = null;

    if(bamStats.getNumberOfProcessedWindows() < bamStats.getNumberOfWindows()){
      int numProcessed = bamStats.getNumberOfProcessedWindows();
            long windowStart = bamStats.getWindowStart(numProcessed);
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Related Classes of org.bioinfo.ngs.qc.qualimap.beans.BamGenomeWindow

  • org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis
  • org.bioinfo.ngs.qc.qualimap.process.ProcessBunchOfReadsTask
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