Package org.broad.igv.sam.reader

Examples of org.broad.igv.sam.reader.FeatureIndex

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    @Test
    public void testIndexSam() throws Exception {
        String samFile = TestUtils.DATA_DIR + "sam/NA12878.muc1.test2.sam";
        String samFileIdx = doStandardIndex(samFile, "sai");

        FeatureIndex idx = SamUtils.getIndexFor(samFile);
        assertTrue(idx.containsChromosome("chr1"));
        assertEquals(1, idx.getIndexedChromosomes().size());
    }
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    /**
     * Test of getIndexedChromosomes method, of class SamIndex.
     */
    @Test
    public void testGetIndexedChromosomes() {
        FeatureIndex idx = new FeatureIndex(f);
        assertTrue(idx.getIndexedChromosomes().size() > 0);
    }
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Related Classes of org.broad.igv.sam.reader.FeatureIndex

  • org.broad.igv.sam.SamIndexTest
  • org.broad.igv.tools.IGVToolsTest
  • org.broad.igv.util.ResourceLocator
  • org.broad.igv.exceptions.DataLoadException
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