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

Examples of org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis

57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
        for (TestConfig test : tests) {

            System.err.println("\nRunning test " + test.getPath() + "\n");


            BamStatsAnalysis bamQc = new BamStatsAnalysis(test.getPathToBamFile()) ;

            String pathToRegionFile = test.getPathToRegionFile();
            if (pathToRegionFile != null && !pathToRegionFile.isEmpty()) {
                bamQc.setSelectedRegions(pathToRegionFile);
                bamQc.setComputeOutsideStats(test.getComputeOutsideStats());
            }

            BamQCRegionReporter bamQcReporter = new BamQCRegionReporter(false, true);


            try {
                bamQc.run();
                bamQcReporter.loadReportData(bamQc.getBamStats());
                bamQcReporter.computeChartsBuffers(bamQc.getBamStats(), bamQc.getLocator(), bamQc.isPairedData());
            } catch (Exception e) {
                assertTrue("Error calculating stats. " + e.getMessage(), false);
                e.printStackTrace();
                return;
            }

            Properties calculatedProps = bamQcReporter.generateBamQcProperties();

            // For generating correct tests
            try {
                calculatedProps.store(new FileOutputStream(test.getResultsPath() + ".new"), null);
            } catch (IOException e) {
                e.printStackTrace();
            }

            compareProperties(calculatedProps, test.getResultsPath());

            if (test.getComputeOutsideStats() && test.getOutsideResultsPath() != null) {
                BamQCRegionReporter outsideReporter = new BamQCRegionReporter(true, false);
                outsideReporter.loadReportData(bamQc.getOutsideBamStats());
                /*outsideReporter.computeChartsBuffers(bamQc.getOutsideBamStats(),
                        bamQc.getLocator(), bamQc.isPairedData());*/
                Properties outsideProps = outsideReporter.generateBamQcProperties();

                /*try {
View Full Code Here
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
    // check outdir
    initOutputDir();

    // init bamqc
    BamStatsAnalysis bamQC = new BamStatsAnalysis(bamFile);

        if(selectedRegionsAvailable){
      bamQC.setSelectedRegions(gffFile);
      bamQC.setComputeOutsideStats(computeOutsideStats);
    }

    // reporting
    bamQC.activeReporting(outdir);
        if (coverageReportFile.length() > 0) {
            bamQC.setPathToCoverageReport(coverageReportFile);
        }

    logger.println("Starting bam qc....");

    // number of windows
    bamQC.setNumberOfWindows(numberOfWindows);
        bamQC.setNumberOfThreads(numThreads);
        bamQC.setNumberOfReadsInBunch(bunchSize);
        bamQC.setProtocol(protocol);
        bamQC.setMinHomopolymerSize(minHomopolymerSize);

    // run evaluation
    bamQC.run();

    logger.println("end of bam qc");

    logger.println("Computing report...");

    BamQCRegionReporter reporter = new BamQCRegionReporter(selectedRegionsAvailable, true);
    reporter.setPaintChromosomeLimits(paintChromosomeLimits);
        if (!genomeToCompare.isEmpty()) {
            reporter.setGenomeGCContentName(genomeToCompare);
        }

        bamQC.prepareInputDescription(reporter, paintChromosomeLimits);

    // 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);
        }

View Full Code Here
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
  public void run() {

    // Create the outputDir directory
    StringBuilder outputDirPath = resultManager.createDirectory();

    BamStatsAnalysis bamQC = new BamStatsAnalysis(bamDialog.getInputFile().getAbsolutePath());

    // Set the number of windows
    bamQC.setNumberOfWindows(bamDialog.getNumberOfWindows());
        bamQC.setNumberOfThreads(bamDialog.getNumThreads());
        bamQC.setNumberOfReadsInBunch(bamDialog.getBunchSize());
        bamQC.setProtocol( bamDialog.getLibraryProtocol() );
        bamQC.setMinHomopolymerSize( bamDialog.getMinHomopolymerSize());

    // Set the region file
        boolean regionsAvailable = false;
    if (bamDialog.getRegionFile() != null) {
      bamQC.setSelectedRegions(bamDialog.getRegionFile().getAbsolutePath());
            bamQC.setComputeOutsideStats(bamDialog.getComputeOutsideRegions());
            regionsAvailable = true;
    }

    // reporting
    bamQC.activeReporting(outputDirPath.toString());

    // setup logging
        AnalysisDialogLoggerThread loggerThread = new AnalysisDialogLoggerThread(bamDialog);
        bamQC.setLoggerThread(loggerThread);

        bamDialog.setUiEnabled(false);
        bamDialog.getProgressStream().setText("Running BAM file analysis...");

    try {

            bamQC.run();
          //timer.cancel();

      bamDialog.getProgressStream().setText("End of bam qc");
            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();
                reporter.setGenomeGCContentName(genomeName);
            }

      bamDialog.getProgressStream().setText("   text report...");
      reporter.loadReportData(bamQC.getBamStats());
      bamDialog.getProgressStream().setText("OK");

      bamDialog.getProgressStream().setText("   charts...");
      reporter.computeChartsBuffers(bamQC.getBamStats(), bamQC.getLocator(), bamQC.isPairedData());
        bamDialog.getProgressStream().setText("OK");


      // Set the reporter into the created tab
      resultManager.addReporter(reporter);

            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();
                    outsideReporter.setGenomeGCContentName(genomeName);
                }

        // save stats
        bamDialog.getProgressStream().setText("   outside text report...");
        outsideReporter.loadReportData(bamQC.getOutsideBamStats());
        bamDialog.getProgressStream().setText("OK");

        // save charts
        bamDialog.getProgressStream().setText("   outside charts...");
        outsideReporter.computeChartsBuffers(bamQC.getOutsideBamStats(), bamQC.getLocator(), bamQC.isPairedData());
        bamDialog.getProgressStream().setText("OK");

        // Set the reporters into the created tab
        resultManager.addReporter(outsideReporter);
            }
View Full Code Here
TOP

Related Classes of org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis

  • org.bioinfo.commons.log.Logger
  • org.bioinfo.formats.core.sequence.Fasta
  • org.bioinfo.formats.core.sequence.io.FastaReader
  • org.bioinfo.ngs.qc.qualimap.beans.BamDetailedGenomeWindow
  • org.bioinfo.ngs.qc.qualimap.beans.BamGenomeWindow
  • org.bioinfo.ngs.qc.qualimap.beans.BamStats
  • org.bioinfo.ngs.qc.qualimap.beans.GenomeLocator
  • org.bioinfo.ngs.qc.qualimap.common.CommandLineBuilder
  • org.bioinfo.ngs.qc.qualimap.gui.threads.BamAnalysisThread
  • org.bioinfo.ngs.qc.qualimap.main.BamQcTool
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.