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

Example 96 with SAMSequenceDictionary

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

the class SplitVcfs method doWork.

@Override
protected Object doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    final ProgressLogger progress = new ProgressLogger(logger, 10000);
    final VCFFileReader fileReader = new VCFFileReader(INPUT);
    final VCFHeader fileHeader = fileReader.getFileHeader();
    final SAMSequenceDictionary sequenceDictionary = SEQUENCE_DICTIONARY != null ? SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).getFileHeader(SEQUENCE_DICTIONARY).getSequenceDictionary() : fileHeader.getSequenceDictionary();
    if (CREATE_INDEX && sequenceDictionary == null) {
        throw new UserException("A sequence dictionary must be available (either through the input file or by setting it explicitly) when creating indexed output.");
    }
    final VariantContextWriterBuilder builder = new VariantContextWriterBuilder().setReferenceDictionary(sequenceDictionary).clearOptions();
    if (CREATE_INDEX)
        builder.setOption(Options.INDEX_ON_THE_FLY);
    try (final VariantContextWriter snpWriter = builder.setOutputFile(SNP_OUTPUT).build();
        final VariantContextWriter indelWriter = builder.setOutputFile(INDEL_OUTPUT).build()) {
        snpWriter.writeHeader(fileHeader);
        indelWriter.writeHeader(fileHeader);
        int incorrectVariantCount = 0;
        final CloseableIterator<VariantContext> iterator = fileReader.iterator();
        while (iterator.hasNext()) {
            final VariantContext context = iterator.next();
            if (context.isIndel())
                indelWriter.add(context);
            else if (context.isSNP())
                snpWriter.add(context);
            else {
                if (STRICT)
                    throw new IllegalStateException("Found a record with type " + context.getType().name());
                else
                    incorrectVariantCount++;
            }
            progress.record(context.getContig(), context.getStart());
        }
        if (incorrectVariantCount > 0) {
            logger.debug("Found " + incorrectVariantCount + " records that didn't match SNP or INDEL");
        }
        CloserUtil.close(iterator);
        CloserUtil.close(fileReader);
    }
    return null;
}

Example 97 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 98 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 99 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 100 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);
}