Examples with LinearIndex htsjdk.tribble.index.linear.LinearIndex used on opensource projects

Example 1 with LinearIndex

use of htsjdk.tribble.index.linear.LinearIndex in project gatk by broadinstitute.

the class IndexFeatureFileIntegrationTest method testVCFIndex.

@Test
public void testVCFIndex() {
    final File ORIG_FILE = getTestFile("test_variants_for_index.vcf");
    final File outName = createTempFile("test_variants_for_index.vcf", ".idx");
    final String[] args = { "--feature_file", ORIG_FILE.getAbsolutePath(), "-O", outName.getAbsolutePath() };
    final Object res = this.runCommandLine(args);
    Assert.assertEquals(res, outName.getAbsolutePath());
    final Index index = IndexFactory.loadIndex(res.toString());
    Assert.assertTrue(index instanceof LinearIndex);
    Assert.assertEquals(index.getSequenceNames(), Arrays.asList("1", "2", "3", "4"));
    checkIndex(index, Arrays.asList("1", "2", "3", "4"));
}

Example 2 with LinearIndex

use of htsjdk.tribble.index.linear.LinearIndex in project gatk by broadinstitute.

the class IndexFeatureFileIntegrationTest method testGVCFIndex.

@Test
public void testGVCFIndex() {
    final File ORIG_FILE = getTestFile("test_variants_for_index.g.vcf");
    final File outName = createTempFile("test_variants_for_index.g.vcf.", ".idx");
    final String[] args = { "--feature_file", ORIG_FILE.getAbsolutePath(), "-O", outName.getAbsolutePath() };
    final Object res = this.runCommandLine(args);
    Assert.assertEquals(res, outName.getAbsolutePath());
    final Index index = IndexFactory.loadIndex(res.toString());
    Assert.assertTrue(index instanceof LinearIndex);
    Assert.assertEquals(index.getSequenceNames(), Arrays.asList("1"));
    checkIndex(index, Arrays.asList("1"));
}

Example 3 with LinearIndex

use of htsjdk.tribble.index.linear.LinearIndex in project gatk by broadinstitute.

the class IndexFeatureFileIntegrationTest method testBCFIndex.

@Test
public void testBCFIndex() {
    final File ORIG_FILE = getTestFile("test_variants_for_index.bcf");
    final File outName = createTempFile("test_variants_for_index.bcf.", ".idx");
    final String[] args = { "--feature_file", ORIG_FILE.getAbsolutePath(), "-O", outName.getAbsolutePath() };
    final Object res = this.runCommandLine(args);
    Assert.assertEquals(res, outName.getAbsolutePath());
    final Index index = IndexFactory.loadIndex(res.toString());
    Assert.assertTrue(index instanceof LinearIndex);
    Assert.assertEquals(index.getSequenceNames(), Arrays.asList("1"));
    checkIndex(index, Arrays.asList("1"));
}

Example 4 with LinearIndex

use of htsjdk.tribble.index.linear.LinearIndex in project gatk by broadinstitute.

the class IndexFeatureFileIntegrationTest method testGVCFTreatedAsVCFIndex.

@Test
public void testGVCFTreatedAsVCFIndex() {
    // Here we're testing what happens when we have a GVCF that is treated by the tool as a
    // regular VCF due to the lack of a .g.vcf extension
    final File ORIG_FILE = getTestFile("test_variants_for_index.gvcf_treated_as_vcf.vcf");
    final File outName = createTempFile("test_variants_for_index.gvcf_treated_as_vcf.vcf.", ".idx");
    final String[] args = { "--feature_file", ORIG_FILE.getAbsolutePath(), "-O", outName.getAbsolutePath() };
    final Object res = this.runCommandLine(args);
    Assert.assertEquals(res, outName.getAbsolutePath());
    final Index index = IndexFactory.loadIndex(res.toString());
    Assert.assertTrue(index instanceof LinearIndex);
    Assert.assertEquals(index.getSequenceNames(), Arrays.asList("1"));
    checkIndex(index, Arrays.asList("1"));
}

Example 5 with LinearIndex

use of htsjdk.tribble.index.linear.LinearIndex in project gatk by broadinstitute.

the class IndexFeatureFileIntegrationTest method testVCFIndex_inferredName.

@Test
public void testVCFIndex_inferredName() {
    final File ORIG_FILE = getTestFile("test_variants_for_index.vcf");
    final String[] args = { "--feature_file", ORIG_FILE.getAbsolutePath() };
    final Object res = this.runCommandLine(args);
    final File tribbleIndex = Tribble.indexFile(ORIG_FILE);
    Assert.assertEquals(res, tribbleIndex.getAbsolutePath());
    tribbleIndex.deleteOnExit();
    final Index index = IndexFactory.loadIndex(res.toString());
    Assert.assertTrue(index instanceof LinearIndex);
    Assert.assertEquals(index.getSequenceNames(), Arrays.asList("1", "2", "3", "4"));
    checkIndex(index, Arrays.asList("1", "2", "3", "4"));
}