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

Example 76 with SAMSequenceDictionary

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

the class IndexUtilsUnitTest method testIsSequenceDictionaryFromIndexNegative.

@Test
public void testIsSequenceDictionaryFromIndexNegative() throws Exception {
    SAMSequenceDictionary dict = new SAMSequenceDictionary();
    dict.addSequence(new SAMSequenceRecord("1", 99));
    dict.addSequence(new SAMSequenceRecord("2", 99));
    Assert.assertFalse(IndexUtils.isSequenceDictionaryFromIndex(dict));
}

Example 77 with SAMSequenceDictionary

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

the class IntervalUtilsUnitTest method testParseUnmappedIntervalArgument.

@Test
public void testParseUnmappedIntervalArgument() {
    final SAMSequenceRecord contigRecord = new SAMSequenceRecord("1", 100);
    final SAMSequenceDictionary dictionary = new SAMSequenceDictionary(Arrays.asList(contigRecord));
    final GenomeLocParser parser = new GenomeLocParser(dictionary);
    List<GenomeLoc> unmappedLoc = IntervalUtils.parseIntervalArguments(parser, "unmapped");
    Assert.assertTrue(unmappedLoc.size() == 1);
    Assert.assertTrue(unmappedLoc.get(0).isUnmapped());
}

Example 78 with SAMSequenceDictionary

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

the class IntervalUtilsUnitTest method testParseUnmappedIntervalArgumentInIntervalFile.

@Test
public void testParseUnmappedIntervalArgumentInIntervalFile() {
    final SAMSequenceRecord contigRecord = new SAMSequenceRecord("1", 100);
    final SAMSequenceDictionary dictionary = new SAMSequenceDictionary(Arrays.asList(contigRecord));
    final GenomeLocParser parser = new GenomeLocParser(dictionary);
    List<GenomeLoc> unmappedLoc = IntervalUtils.parseIntervalArguments(parser, publicTestDir + "org/broadinstitute/hellbender/engine/reads_data_source_test1_unmapped.intervals");
    Assert.assertTrue(unmappedLoc.size() == 1);
    Assert.assertTrue(unmappedLoc.get(0).isUnmapped());
}

Example 79 with SAMSequenceDictionary

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

the class IntervalUtilsUnitTest method testCompareLocatables.

@Test
public void testCompareLocatables() throws Exception {
    final SAMSequenceDictionary dict = new SAMSequenceDictionary();
    dict.addSequence(new SAMSequenceRecord("1", 1000));
    dict.addSequence(new SAMSequenceRecord("2", 1000));
    final SimpleInterval chr1_1_100 = new SimpleInterval("1:1-100");
    final SimpleInterval chr1_5_100 = new SimpleInterval("1:5-100");
    final SimpleInterval chr2_1_100 = new SimpleInterval("2:1-100");
    // equal intervals comparison return 0
    Assert.assertEquals(IntervalUtils.compareLocatables(chr1_1_100, chr1_1_100, dict), 0);
    Assert.assertEquals(IntervalUtils.compareLocatables(chr1_5_100, chr1_5_100, dict), 0);
    Assert.assertEquals(IntervalUtils.compareLocatables(chr2_1_100, chr2_1_100, dict), 0);
    // first < second return negative
    Assert.assertTrue(IntervalUtils.compareLocatables(chr1_1_100, chr1_5_100, dict) < 0);
    Assert.assertTrue(IntervalUtils.compareLocatables(chr1_1_100, chr2_1_100, dict) < 0);
    Assert.assertTrue(IntervalUtils.compareLocatables(chr1_5_100, chr2_1_100, dict) < 0);
    // first > second return positive
    Assert.assertTrue(IntervalUtils.compareLocatables(chr2_1_100, chr1_1_100, dict) > 0);
    Assert.assertTrue(IntervalUtils.compareLocatables(chr2_1_100, chr1_5_100, dict) > 0);
    Assert.assertTrue(IntervalUtils.compareLocatables(chr1_5_100, chr1_1_100, dict) > 0);
}

Example 80 with SAMSequenceDictionary

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

the class IntervalUtilsUnitTest method testIntervalIsOnDictionaryContigNullInterval.

@Test(expectedExceptions = IllegalArgumentException.class)
public void testIntervalIsOnDictionaryContigNullInterval() {
    final SAMSequenceDictionary dictionary = new SAMSequenceDictionary(Arrays.asList(new SAMSequenceRecord("1", 1000)));
    IntervalUtils.intervalIsOnDictionaryContig(null, dictionary);
}