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

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

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            outdir = parentDir + File.separator + "countsQC_results";
        }
        // init output dir
        initOutputDir();

        AnalysisResultManager resultManager = new AnalysisResultManager(AnalysisType.COUNTS_QC);

        ArrayList<String> conditionNames = new ArrayList<String>();
        List<CountsSampleInfo> samples = CountsQcAnalysis.parseInputFile(inputFile, conditionNames);
        if (samples.size() == 0) {
            System.err.println("The input file " + inputFile + " does not contain any samples. " +
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    @Override
    protected void execute() throws Exception {

        initOutputDir();

        AnalysisResultManager resultManager = new AnalysisResultManager(AnalysisType.CLUSTERING);

        EpiAnalysis epiAnalysis = new EpiAnalysis(resultManager,homePath,cfg);

        LoggerThread loggerThread = new LoggerThread() {
            public void logLine(String msg) {
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    @Override
    protected void execute() throws Exception {

        initOutputDir();

        AnalysisResultManager resultManager = new AnalysisResultManager(AnalysisType.MULTISAMPLE_BAM_QC);

        List<SampleInfo> bamQcResults = MultisampleBamQcAnalysis.parseInputFile(inputFile);
        if (bamQcResults.size() == 0) {
            System.err.println("The input file " + inputFile + " does not contain any samples. " +
                    "Please check file format.");
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    // save stats

        reporter.writeReport(bamQC.getBamStats(),outdir);

        AnalysisResultManager resultManager = new AnalysisResultManager(AnalysisType.BAM_QC);

        reporter.loadReportData(bamQC.getBamStats());
        reporter.computeChartsBuffers(bamQC.getBamStats(), bamQC.getLocator(), bamQC.isPairedData());
        resultManager.addReporter(reporter);

        if(selectedRegionsAvailable && computeOutsideStats){

            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());

            resultManager.addReporter(outsideReporter);
        }


        exportResult(resultManager);
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        ComputeCountsTask computeCountsTask = new ComputeCountsTask(bamFile, gffFile);
        computeCountsTask.setProtocol(LibraryProtocol.getProtocolByName(protocol));
        computeCountsTask.setCountingAlgorithm(alg);
        computeCountsTask.setCollectRnaSeqStats(true);

        AnalysisResultManager resultManager = new AnalysisResultManager(AnalysisType.RNA_SEQ_QC);

        RNASeqQCAnalysis rnaSeqQCAnalysis = new RNASeqQCAnalysis(resultManager, computeCountsTask);
        if (countsFile.length() > 0) {
            rnaSeqQCAnalysis.setCountsFilePath(countsFile);
        }
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Related Classes of org.bioinfo.ngs.qc.qualimap.beans.AnalysisResultManager

  • org.bioinfo.ngs.qc.qualimap.main.BamQcTool
  • org.bioinfo.ngs.qc.qualimap.main.CountsQcTool
  • org.bioinfo.ngs.qc.qualimap.main.EpiTool
  • org.bioinfo.ngs.qc.qualimap.main.MultisampleBamQcTool
  • org.bioinfo.ngs.qc.qualimap.main.RnaSeqQcTool
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