Package org.broad.igv.sam.reader

Examples of org.broad.igv.sam.reader.FeatureIndex.containsChromosome()

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    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());
    }

    @Test
    public void testIndexFasta() throws Exception {
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