Package org.broad.igv.track

Examples of org.broad.igv.track.TribbleFeatureSource

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public class VCFVariantTest extends AbstractHeadlessTest {

    private VCFVariant get_hc_mod_Feat(String chr, int start, int end) throws Exception{
        String filePath = TestUtils.DATA_DIR + "vcf/hc_mod.vcf";
        TestUtils.createIndex(filePath);
        TribbleFeatureSource src = TribbleFeatureSource.getFeatureSource(new ResourceLocator(filePath), genome);

        return (VCFVariant) (src.getFeatures(chr, start, end)).next();
    }
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    public void testMissingFieldInCommaSeparated() throws Exception{

        String filePath = TestUtils.DATA_DIR + "vcf/missingFields.vcf";
        TestUtils.createIndex(filePath);

        TribbleFeatureSource src = TribbleFeatureSource.getFeatureSource(new ResourceLocator(filePath), genome);

        Iterator iter = src.getFeatures("chr2", 3321000, 13346000);

        int count = 0;
        boolean found = false;

        while(iter.hasNext()){
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    public void testGFFWithFasta() throws Exception {

        String path = TestUtils.DATA_DIR + "gff/gffWithFasta.gff";
        final ResourceLocator locator = new ResourceLocator(path);

        TribbleFeatureSource tribbleFeatureSource = TribbleFeatureSource.getFeatureSource(locator, genome);
        FeatureSource source = new GFFFeatureSource(tribbleFeatureSource);

        int featureCount = 0;
        Iterator<Feature> iter = source.getFeatures("chr7", 0, Integer.MAX_VALUE);
        while (iter.hasNext()) {
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Related Classes of org.broad.igv.track.TribbleFeatureSource

  • org.broad.igv.data.DataTile
  • org.broad.igv.feature.BasicFeature
  • org.broad.igv.feature.tribble.GFFCodecTest
  • org.broad.igv.feature.tribble.VCFWrapperCodecTest
  • org.broad.igv.tdf.TDFDataSource
  • org.broad.igv.tdf.TDFReader
  • org.broad.igv.ui.util.IndexCreatorDialog
  • org.broad.igv.variant.vcf.VCFVariantTest
  • java.io.File
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