Package org.broad.igv.tools

Examples of org.broad.igv.tools.IgvTools

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     * @param indexType
     * @param binSize
     * @throws IOException
     */
    public static void createIndex(String file, int indexType, int binSize) throws IOException {
        String indexPath = (new IgvTools()).doIndex(file, null, indexType, binSize);
        File indexFile = new File(indexPath);
        indexFile.deleteOnExit();
    }
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        File chosenFile = chooseFile();
        outputField.setText(chosenFile.getAbsolutePath());
    }

    private void initUI() {
        this.igvTools = new IgvTools();
        setContentPane(mainPanel);
        setModal(true);

        addWindowListener(new WindowAdapter() {
            public void windowClosing(WindowEvent windowEvent) {
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    IgvTools igvTools;

    public IndexGui() {

        this.igvTools = new IgvTools();
        initComponents();

        setTitle("Create Index");

        // Hide output file field for now
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    IgvTools igvTools;

    @Before
    public void setUp() throws Exception {
        Globals.setHeadless(true);
        igvTools = new IgvTools();
    }
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        return tstOperationBED(pathA, pathB, operation, expectedNumFeatures);
    }

    private List<Feature> tstOperationBED(String pathA, String pathB,
                                          CombinedFeatureSource.Operation operation, int expectedNumFeatures) throws Exception {
        IgvTools igvTools = new IgvTools();
        igvTools.doIndex(pathA, null, 1, 16000);
        igvTools.doIndex(pathB, null, 1, 16000);
        FeatureSource sourceA = TribbleFeatureSource.getFeatureSource(new ResourceLocator(pathA), genome);
        FeatureSource sourceB = TribbleFeatureSource.getFeatureSource(new ResourceLocator(pathB), genome);


        CombinedFeatureSource combinedFeatureSource = new CombinedFeatureSource(new FeatureSource[]{sourceA, sourceB}, operation);
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Related Classes of org.broad.igv.tools.IgvTools

  • htsjdk.tribble.FeatureCodec
  • htsjdk.tribble.index.Index
  • htsjdk.tribble.util.LittleEndianOutputStream
  • jargs.gnu.CmdLineParser
  • org.broad.igv.feature.genome.Genome
  • org.broad.igv.feature.genome.GenomeDescriptor
  • org.broad.igv.feature.genome.GenomeManager
  • org.broad.igv.feature.GFFParser
  • org.broad.igv.feature.tribble.GFFCodec
  • org.broad.igv.feature.tribble.IGVBEDCodec
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