Examples with SAMSequenceDictionary htsjdk.samtools.SAMSequenceDictionary used on opensource projects

Example 6 with SAMSequenceDictionary

use of htsjdk.samtools.SAMSequenceDictionary in project gatk by broadinstitute.

the class GenomeLocParserUnitTest method testcreateGenomeLocOnContig.

@Test
public void testcreateGenomeLocOnContig() throws FileNotFoundException {
    final CachingIndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(exampleReference));
    final SAMSequenceDictionary dict = seq.getSequenceDictionary();
    final GenomeLocParser genomeLocParser = new GenomeLocParser(dict);
    for (final SAMSequenceRecord rec : dict.getSequences()) {
        final GenomeLoc loc = genomeLocParser.createOverEntireContig(rec.getSequenceName());
        Assert.assertEquals(loc.getContig(), rec.getSequenceName());
        Assert.assertEquals(loc.getStart(), 1);
        Assert.assertEquals(loc.getStop(), rec.getSequenceLength());
    }
}

Example 7 with SAMSequenceDictionary

use of htsjdk.samtools.SAMSequenceDictionary in project gatk by broadinstitute.

the class IndexUtilsUnitTest method testCreateSequenceDictionaryFromTabixIndex.

@Test
public void testCreateSequenceDictionaryFromTabixIndex() throws Exception {
    final SAMSequenceDictionary dict = IndexUtils.createSequenceDictionaryFromFeatureIndex(new File(getToolTestDataDir(), "test_variants_for_index.vcf.bgz"));
    final Set<String> contigs = dict.getSequences().stream().map(s -> s.getSequenceName()).collect(Collectors.toSet());
    Assert.assertEquals(contigs, Sets.newHashSet("1", "2", "3", "4"));
}

Example 8 with SAMSequenceDictionary

use of htsjdk.samtools.SAMSequenceDictionary in project gatk by broadinstitute.

the class GenomeLocParserUnitTest method testContigHasColon.

@Test
public void testContigHasColon() {
    SAMFileHeader header = new SAMFileHeader();
    header.setSortOrder(htsjdk.samtools.SAMFileHeader.SortOrder.coordinate);
    SAMSequenceDictionary dict = new SAMSequenceDictionary();
    SAMSequenceRecord rec = new SAMSequenceRecord("c:h:r1", 10);
    rec.setSequenceLength(10);
    dict.addSequence(rec);
    header.setSequenceDictionary(dict);
    final GenomeLocParser myGenomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
    GenomeLoc loc = myGenomeLocParser.parseGenomeLoc("c:h:r1:4-5");
    assertEquals(0, loc.getContigIndex());
    assertEquals(loc.getStart(), 4);
    assertEquals(loc.getStop(), 5);
}

Example 9 with SAMSequenceDictionary

use of htsjdk.samtools.SAMSequenceDictionary in project gatk by broadinstitute.

the class IndexUtilsUnitTest method testCreateSequenceDictionaryFromTribbleIndex.

@Test
public void testCreateSequenceDictionaryFromTribbleIndex() throws Exception {
    final SAMSequenceDictionary dict = IndexUtils.createSequenceDictionaryFromFeatureIndex(new File(getToolTestDataDir(), "test_variants_for_index.vcf"));
    final Set<String> contigs = dict.getSequences().stream().map(s -> s.getSequenceName()).collect(Collectors.toSet());
    Assert.assertEquals(contigs, Sets.newHashSet("1", "2", "3", "4"));
}

Example 10 with SAMSequenceDictionary

use of htsjdk.samtools.SAMSequenceDictionary in project gatk by broadinstitute.

the class IndexUtilsUnitTest method testIsSequenceDictionaryFromIndexPositive.

@Test
public void testIsSequenceDictionaryFromIndexPositive() throws Exception {
    final SAMSequenceDictionary dict = IndexUtils.createSequenceDictionaryFromFeatureIndex(new File(getToolTestDataDir(), "test_variants_for_index.vcf"));
    Assert.assertTrue(IndexUtils.isSequenceDictionaryFromIndex(dict));
}