Package org.broad.igv.track

Examples of org.broad.igv.track.MutationTrack


        //A2M  2  genome.wustl.edu  36  12  9150104  9150104  +  Missense_Mutation  SNP  C  C  G  Unknown  Unknown  TCGA-02-0024-01B-01W  TCGA-02-0024-10A-01W  C  C  C  G  C  C  Valid  Valid  Somatic  Phase_I

        //There should be 1 track per sampleId
        Set<String> sampleIds = new HashSet<String>(trackList.size());
        for (FeatureTrack track : trackList) {
            MutationTrack mutTrack = (MutationTrack) track;

            assertFalse(sampleIds.contains(mutTrack.getName()));

            sampleIds.add(mutTrack.getName());
            if (mutTrack.getName().equals(testSampleId)) {
                List<Feature> features = mutTrack.getFeatures("chr12", testStart, testEnd);
                assertEquals(1, features.size());
                Mutation mut = (Mutation) features.get(0);

                assertEquals(testSampleId, mut.getSampleId());
                assertEquals(testChr, mut.getChr());
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