Package htsjdk.tribble

Examples of htsjdk.tribble.Feature

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        Iterator<Feature> feats = source.getFeatures(chr, start, end);
        List<Feature> sourceFeats = new ArrayList<Feature>(2);

        while (feats.hasNext()) {
            Feature feat = feats.next();
            assertEquals(chr, feat.getChr());
            sourceFeats.add(feat);
        }
        return sourceFeats;
    }
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        try {
            GFFFeatureSource source = getGffFeatureSource(filepath);

            Iterator<Feature> iter = source.getFeatures("chr1", 0, Integer.MAX_VALUE);
            int featureCount = 0;
            Feature feature = null;
            while (iter.hasNext()) {
                feature = iter.next();
                featureCount++;
            }
            assertEquals(1, featureCount);
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            testGetter(name, v1, test.expected(name), true, tracker);

            List<Feature> v2 = name.equals("A+B") ? tracker.getValues(Feature.class, locus) : tracker.getValues(Feature.class, name, locus);
            testGetter(name, v2, startingHere(test.expected(name)), true, tracker);

            Feature v3 = name.equals("A+B") ? tracker.getFirstValue(Feature.class) : tracker.getFirstValue(Feature.class, name);
            testGetter(name, Arrays.asList(v3), test.expected(name), false, tracker);

            Feature v4 = name.equals("A+B") ? tracker.getFirstValue(Feature.class, locus) : tracker.getFirstValue(Feature.class, name, locus);
            testGetter(name, Arrays.asList(v4), startingHere(test.expected(name)), false, tracker);
        }
    }
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            testGetter(nameAsString, v1, test.expected(nameAsString), true, tracker);

            List<Feature> v2 = tracker.getValues(binding, locus);
            testGetter(nameAsString, v2, startingHere(test.expected(nameAsString)), true, tracker);

            Feature v3 = tracker.getFirstValue(binding);
            testGetter(nameAsString, Arrays.asList(v3), test.expected(nameAsString), false, tracker);

            Feature v4 = tracker.getFirstValue(binding, locus);
            testGetter(nameAsString, Arrays.asList(v4), startingHere(test.expected(nameAsString)), false, tracker);
        }
    }
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        testGetter(nameAsString, v1, test.expected(nameAsString), true, tracker);

        List<Feature> v2 = tracker.getValues(binding, locus);
        testGetter(nameAsString, v2, startingHere(test.expected(nameAsString)), true, tracker);

        Feature v3 = tracker.getFirstValue(binding);
        testGetter(nameAsString, Arrays.asList(v3), test.expected(nameAsString), false, tracker);

        Feature v4 = tracker.getFirstValue(binding, locus);
        testGetter(nameAsString, Arrays.asList(v4), startingHere(test.expected(nameAsString)), false, tracker);
    }
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        Assert.assertEquals(loc.getStop(), read.getAlignmentStart());
    }

    @Test
    public void testCreationFromFeature() {
        final Feature feature = new BasicFeature("chr1", 1, 5);
        final GenomeLoc loc = genomeLocParser.createGenomeLoc(feature);
        Assert.assertEquals(loc.getContig(), feature.getChr());
        Assert.assertEquals(loc.getStart(), feature.getStart());
        Assert.assertEquals(loc.getStop(), feature.getEnd());
    }
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                if ( samples.isEmpty() ) {
                    List<Feature> features = tracker.getValues(variants, loc);
                    if ( features.size() == 0 )
                        throw new IllegalStateException("No rod data is present, but we just created a VariantContext");

                    Feature f = features.get(0);
                    if ( f instanceof RawHapMapFeature )
                        samples.addAll(Arrays.asList(((RawHapMapFeature)f).getSampleIDs()));
                    else
                        samples.addAll(vc.getSampleNames());
                }
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