Examples of AnalysisResultManager

org.bioinfo.ngs.qc.qualimap.beans.AnalysisResultManager
Created by kokonech Date: 7/13/13 Time: 3:34 PM

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

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

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

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


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

        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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