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

Example 31 with SAMSequenceDictionary

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

the class GATKToolUnitTest method testBestSequenceDictionary_fromReads.

@Test
public void testBestSequenceDictionary_fromReads() throws Exception {
    final GATKTool tool = new TestGATKToolWithReads();
    final CommandLineParser clp = new CommandLineArgumentParser(tool);
    final File bamFile = new File(publicTestDir + "org/broadinstitute/hellbender/engine/reads_data_source_test1.bam");
    final String[] args = { "-I", bamFile.getCanonicalPath() };
    clp.parseArguments(System.out, args);
    tool.onStartup();
    //read the dict back in and compare to bam dict
    final SAMSequenceDictionary toolDict = tool.getBestAvailableSequenceDictionary();
    try (final SamReader open = SamReaderFactory.makeDefault().open(bamFile)) {
        final SAMSequenceDictionary bamDict = open.getFileHeader().getSequenceDictionary();
        toolDict.assertSameDictionary(bamDict);
        bamDict.assertSameDictionary(toolDict);
        Assert.assertEquals(toolDict, bamDict);
    }
}

Example 32 with SAMSequenceDictionary

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

the class AddContextDataToReadSparkUnitTest method addContextDataTest.

@Test(dataProvider = "bases", groups = "spark")
public void addContextDataTest(List<GATKRead> reads, List<GATKVariant> variantList, List<KV<GATKRead, ReadContextData>> expectedReadContextData, JoinStrategy joinStrategy) throws IOException {
    JavaSparkContext ctx = SparkContextFactory.getTestSparkContext();
    JavaRDD<GATKRead> rddReads = ctx.parallelize(reads);
    JavaRDD<GATKVariant> rddVariants = ctx.parallelize(variantList);
    ReferenceMultiSource mockSource = mock(ReferenceMultiSource.class, withSettings().serializable());
    when(mockSource.getReferenceBases(any(PipelineOptions.class), any())).then(new ReferenceBasesAnswer());
    when(mockSource.getReferenceWindowFunction()).thenReturn(ReferenceWindowFunctions.IDENTITY_FUNCTION);
    SAMSequenceDictionary sd = new SAMSequenceDictionary(Lists.newArrayList(new SAMSequenceRecord("1", 100000), new SAMSequenceRecord("2", 100000)));
    when(mockSource.getReferenceSequenceDictionary(null)).thenReturn(sd);
    JavaPairRDD<GATKRead, ReadContextData> rddActual = AddContextDataToReadSpark.add(ctx, rddReads, mockSource, rddVariants, joinStrategy, sd, 10000, 1000);
    Map<GATKRead, ReadContextData> actual = rddActual.collectAsMap();
    Assert.assertEquals(actual.size(), expectedReadContextData.size());
    for (KV<GATKRead, ReadContextData> kv : expectedReadContextData) {
        ReadContextData readContextData = actual.get(kv.getKey());
        Assert.assertNotNull(readContextData);
        Assert.assertTrue(CollectionUtils.isEqualCollection(Lists.newArrayList(readContextData.getOverlappingVariants()), Lists.newArrayList(kv.getValue().getOverlappingVariants())));
        SimpleInterval minimalInterval = kv.getValue().getOverlappingReferenceBases().getInterval();
        ReferenceBases subset = readContextData.getOverlappingReferenceBases().getSubset(minimalInterval);
        Assert.assertEquals(subset, kv.getValue().getOverlappingReferenceBases());
    }
}

Example 33 with SAMSequenceDictionary

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

the class FindBadGenomicKmersSparkUnitTest method miniRefTest.

@Test(groups = "spark")
public void miniRefTest() throws IOException {
    final JavaSparkContext ctx = SparkContextFactory.getTestSparkContext();
    final ReferenceMultiSource ref = new ReferenceMultiSource((PipelineOptions) null, REFERENCE_FILE_NAME, ReferenceWindowFunctions.IDENTITY_FUNCTION);
    final SAMSequenceDictionary dict = ref.getReferenceSequenceDictionary(null);
    if (dict == null)
        throw new GATKException("No reference dictionary available.");
    final Map<SVKmer, Long> kmerMap = new LinkedHashMap<>();
    for (final SAMSequenceRecord rec : dict.getSequences()) {
        final SimpleInterval interval = new SimpleInterval(rec.getSequenceName(), 1, rec.getSequenceLength());
        final byte[] bases = ref.getReferenceBases(null, interval).getBases();
        final SVKmerizer kmerizer = new SVKmerizer(bases, KMER_SIZE, new SVKmerLong());
        while (kmerizer.hasNext()) {
            final SVKmer kmer = kmerizer.next().canonical(KMER_SIZE);
            final Long currentCount = kmerMap.getOrDefault(kmer, 0L);
            kmerMap.put(kmer, currentCount + 1);
        }
    }
    final Iterator<Map.Entry<SVKmer, Long>> kmerIterator = kmerMap.entrySet().iterator();
    while (kmerIterator.hasNext()) {
        if (kmerIterator.next().getValue() <= FindBadGenomicKmersSpark.MAX_KMER_FREQ)
            kmerIterator.remove();
    }
    final List<SVKmer> badKmers = FindBadGenomicKmersSpark.findBadGenomicKmers(ctx, KMER_SIZE, Integer.MAX_VALUE, ref, null, null);
    final Set<SVKmer> badKmerSet = new HashSet<>(badKmers);
    Assert.assertEquals(badKmers.size(), badKmerSet.size());
    Assert.assertEquals(badKmerSet, kmerMap.keySet());
}

Example 34 with SAMSequenceDictionary

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

the class SequenceDictionaryUtilsUnitTest method testSequenceDictionaryValidation.

@Test(dataProvider = "SequenceDictionaryDataProvider")
public void testSequenceDictionaryValidation(final List<SAMSequenceRecord> firstDictionaryContigs, final List<SAMSequenceRecord> secondDictionaryContigs, //not needed by this test
final SequenceDictionaryUtils.SequenceDictionaryCompatibility dictionaryCompatibility, final Class<? extends UserException> expectedExceptionUponValidation, final boolean requireSuperset, final boolean checkContigOrdering) {
    final SAMSequenceDictionary firstDictionary = createSequenceDictionary(firstDictionaryContigs);
    final SAMSequenceDictionary secondDictionary = createSequenceDictionary(secondDictionaryContigs);
    final String testDescription = String.format("First dictionary: %s  Second dictionary: %s", SequenceDictionaryUtils.getDictionaryAsString(firstDictionary), SequenceDictionaryUtils.getDictionaryAsString(secondDictionary));
    Exception exceptionThrown = null;
    try {
        SequenceDictionaryUtils.validateDictionaries("firstDictionary", firstDictionary, "secondDictionary", secondDictionary, requireSuperset, checkContigOrdering);
    } catch (Exception e) {
        exceptionThrown = e;
    }
    if (expectedExceptionUponValidation != null) {
        Assert.assertTrue(exceptionThrown != null && expectedExceptionUponValidation.isInstance(exceptionThrown), String.format("Expected exception %s but saw %s instead. %s", expectedExceptionUponValidation.getSimpleName(), exceptionThrown == null ? "no exception" : exceptionThrown.getClass().getSimpleName(), testDescription));
    } else {
        Assert.assertTrue(exceptionThrown == null, String.format("Expected no exception but saw exception %s instead. %s", exceptionThrown != null ? exceptionThrown.getClass().getSimpleName() : "none", testDescription));
    }
}

Example 35 with SAMSequenceDictionary

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

the class SequenceDictionaryUtilsUnitTest method testStandardValidationDoesNotRequireSuperset.

@Test(dataProvider = "NonSupersetData")
public void testStandardValidationDoesNotRequireSuperset(final List<SAMSequenceRecord> firstDictionaryContigs, final List<SAMSequenceRecord> secondDictionaryContigs) {
    final SAMSequenceDictionary firstDictionary = createSequenceDictionary(firstDictionaryContigs);
    final SAMSequenceDictionary secondDictionary = createSequenceDictionary(secondDictionaryContigs);
    // Standard validation (the overload of validateDictionaries() that doesn't take any boolean args)
    // should not require a superset relationship, so we shouldn't get an exception here
    SequenceDictionaryUtils.validateDictionaries("first", firstDictionary, "second", secondDictionary);
}