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

Example 56 with SAMSequenceRecord

use of htsjdk.samtools.SAMSequenceRecord 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 57 with SAMSequenceRecord

use of htsjdk.samtools.SAMSequenceRecord 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 58 with SAMSequenceRecord

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

the class IntervalUtilsUnitTest method testIntervalFileToListInvalidPicardIntervalHandling.

@Test(expectedExceptions = UserException.CouldNotReadInputFile.class, dataProvider = "invalidIntervalTestData")
public void testIntervalFileToListInvalidPicardIntervalHandling(GenomeLocParser genomeLocParser, String contig, int intervalStart, int intervalEnd) throws Exception {
    final SAMFileHeader picardFileHeader = new SAMFileHeader();
    picardFileHeader.addSequence(genomeLocParser.getContigInfo("1"));
    picardFileHeader.addSequence(new SAMSequenceRecord("2", 100000));
    final IntervalList picardIntervals = new IntervalList(picardFileHeader);
    picardIntervals.add(new Interval(contig, intervalStart, intervalEnd, true, "dummyname"));
    final File picardIntervalFile = createTempFile("testIntervalFileToListInvalidPicardIntervalHandling", ".intervals");
    picardIntervals.write(picardIntervalFile);
    // loadIntervals() will validate all intervals against the sequence dictionary in our genomeLocParser,
    // and should throw for all intervals in our invalidIntervalTestData set
    IntervalUtils.intervalFileToList(genomeLocParser, picardIntervalFile.getAbsolutePath());
}

Example 59 with SAMSequenceRecord

use of htsjdk.samtools.SAMSequenceRecord 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 60 with SAMSequenceRecord

use of htsjdk.samtools.SAMSequenceRecord 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);
}