Package org.broad.igv.tools

Examples of org.broad.igv.tools.IgvTools.doIndex()

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    }

    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);

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    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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