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

Example 26 with SAMRecord

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

the class AlignedAssemblyUnitTest method testConstructionFromSAMRecord.

@Test(dataProvider = "AlignmentIntervalCtorTestForSimpleInversion", groups = "sv")
public void testConstructionFromSAMRecord(final BwaMemAlignment bwaMemAlignment, final SimpleInterval expectedReferenceInterval, final Cigar expectedCigar, final boolean expectedIsPositiveStrand, final int expectedStartOnContig_1BasedInclusive, final int expectedEndOnContig_1BasedInclusive, final int expectedContigLength, final int expectedMapQualInBwaMemAlignment, final AlignedAssembly.AlignmentInterval expectedAlignmentInterval) {
    final SAMRecord samRecord = BwaMemAlignmentUtils.applyAlignment("whatever", SVDiscoveryTestDataProvider.makeDummySequence(expectedContigLength, (byte) 'A'), null, null, bwaMemAlignment, refNames, hg19Header, false, false);
    final AlignedAssembly.AlignmentInterval alignmentInterval = new AlignedAssembly.AlignmentInterval(samRecord);
    Assert.assertEquals(alignmentInterval.referenceInterval, expectedReferenceInterval);
    Assert.assertEquals(alignmentInterval.cigarAlong5to3DirectionOfContig, expectedCigar);
    Assert.assertEquals(alignmentInterval.forwardStrand, expectedIsPositiveStrand);
    Assert.assertEquals(alignmentInterval.startInAssembledContig, expectedStartOnContig_1BasedInclusive);
    Assert.assertEquals(alignmentInterval.endInAssembledContig, expectedEndOnContig_1BasedInclusive);
    Assert.assertEquals(alignmentInterval.mapQual, Math.max(SAMRecord.NO_MAPPING_QUALITY, expectedMapQualInBwaMemAlignment));
    Assert.assertEquals(alignmentInterval, expectedAlignmentInterval);
}

Example 27 with SAMRecord

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

the class SamReaderQueryingIterator method next.

@Override
public SAMRecord next() {
    if (nextRecord == null) {
        throw new NoSuchElementException("Iterator is exhausted");
    }
    final SAMRecord toReturn = nextRecord;
    nextRecord = loadNextRecord();
    return toReturn;
}

Example 28 with SAMRecord

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

the class RevertBaseQualityScoresIntegrationTest method hasOriginalQualScores.

private static boolean hasOriginalQualScores(final File bam) throws IOException {
    try (final SamReader reader = SamReaderFactory.makeDefault().open(bam)) {
        for (SAMRecord read : reader) {
            final byte[] originalBaseQualities = read.getOriginalBaseQualities();
            Assert.assertNotNull(originalBaseQualities);
            final byte[] baseQualities = read.getBaseQualities();
            Assert.assertEquals(originalBaseQualities.length, baseQualities.length);
            for (int i = 0; i < originalBaseQualities.length; ++i) {
                if (originalBaseQualities[i] != baseQualities[i]) {
                    return false;
                }
            }
        }
    }
    return true;
}

Example 29 with SAMRecord

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

the class UnmarkDuplicatesIntegrationTest method getDuplicateCountForBam.

private static int getDuplicateCountForBam(final File bam, final File referenceFile) throws IOException {
    int duplicateCount = 0;
    final SamReaderFactory factory = SamReaderFactory.makeDefault();
    if (referenceFile != null) {
        factory.referenceSequence(referenceFile);
    }
    try (final SamReader reader = factory.open(bam)) {
        for (SAMRecord read : reader) {
            if (read.getDuplicateReadFlag()) {
                ++duplicateCount;
            }
        }
    }
    return duplicateCount;
}

Example 30 with SAMRecord

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

the class ReadsSparkSink method writeReadsADAM.

private static void writeReadsADAM(final JavaSparkContext ctx, final String outputFile, final JavaRDD<SAMRecord> reads, final SAMFileHeader header) throws IOException {
    final SequenceDictionary seqDict = SequenceDictionary.fromSAMSequenceDictionary(header.getSequenceDictionary());
    final RecordGroupDictionary readGroups = RecordGroupDictionary.fromSAMHeader(header);
    final JavaPairRDD<Void, AlignmentRecord> rddAlignmentRecords = reads.map(read -> {
        read.setHeaderStrict(header);
        AlignmentRecord alignmentRecord = GATKReadToBDGAlignmentRecordConverter.convert(read, seqDict, readGroups);
        read.setHeaderStrict(null);
        return alignmentRecord;
    }).mapToPair(alignmentRecord -> new Tuple2<>(null, alignmentRecord));
    // instantiating a Job is necessary here in order to set the Hadoop Configuration...
    final Job job = Job.getInstance(ctx.hadoopConfiguration());
    // ...here, which sets a config property that the AvroParquetOutputFormat needs when writing data. Specifically,
    // we are writing the Avro schema to the Configuration as a JSON string. The AvroParquetOutputFormat class knows
    // how to translate objects in the Avro data model to the Parquet primitives that get written.
    AvroParquetOutputFormat.setSchema(job, AlignmentRecord.getClassSchema());
    deleteHadoopFile(outputFile, ctx.hadoopConfiguration());
    rddAlignmentRecords.saveAsNewAPIHadoopFile(outputFile, Void.class, AlignmentRecord.class, AvroParquetOutputFormat.class, job.getConfiguration());
}