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

Example 11 with SAMFileHeader

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

the class ReadPileupUnitTest method testSplitBySampleMissingReadGroupException.

@Test(expectedExceptions = UserException.ReadMissingReadGroup.class)
public void testSplitBySampleMissingReadGroupException() throws Exception {
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader(1, 1, 1000);
    final GATKRead read = ArtificialReadUtils.createArtificialRead(header, "nullRG", 0, 1, 10);
    final ReadPileup pileup = new ReadPileup(loc, Collections.singletonList(read), 1);
    final Map<String, ReadPileup> error = pileup.splitBySample(header, null);
}

Example 12 with SAMFileHeader

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

the class ReadPileupUnitTest method testInvalidConstructorParametersReadsAndOffsetsLists.

@Test(expectedExceptions = IllegalArgumentException.class)
public void testInvalidConstructorParametersReadsAndOffsetsLists() {
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader(1, 1, 1000);
    final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, "read1", 0, 1, 10);
    new ReadPileup(loc, Arrays.asList(read1), Arrays.asList(1, 2, 3));
}

Example 13 with SAMFileHeader

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

the class ReadPileupUnitTest method testNullConstructorParametersLoc.

@Test(expectedExceptions = IllegalArgumentException.class)
public void testNullConstructorParametersLoc() {
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader(1, 1, 1000);
    final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, "read1", 0, 1, 10);
    new ReadPileup(null, Arrays.asList(read1), Arrays.asList(1));
}

Example 14 with SAMFileHeader

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

the class LocusWalker method traverse.

/**
     * Implementation of locus-based traversal.
     * Subclasses can override to provide their own behavior but default implementation should be suitable for most uses.
     *
     * The default implementation iterates over all positions in the reference covered by reads (filtered and transformed)
     * for all samples in the read groups, using the downsampling method provided by {@link #getDownsamplingInfo()}
     * and including deletions only if {@link #includeDeletions()} returns {@code true}.
     */
@Override
public void traverse() {
    final SAMFileHeader header = getHeaderForReads();
    // get the samples from the read groups
    final Set<String> samples = header.getReadGroups().stream().map(SAMReadGroupRecord::getSample).collect(Collectors.toSet());
    final CountingReadFilter countedFilter = makeReadFilter();
    // get the filter and transformed iterator
    final Iterator<GATKRead> readIterator = getTransformedReadStream(countedFilter).iterator();
    // get the LIBS
    final LocusIteratorByState libs = new LocusIteratorByState(readIterator, getDownsamplingInfo(), keepUniqueReadListInLibs(), samples, header, includeDeletions(), includeNs());
    final Iterator<AlignmentContext> iterator = createAlignmentContextIterator(header, libs);
    // iterate over each alignment, and apply the function
    final Spliterator<AlignmentContext> spliterator = Spliterators.spliteratorUnknownSize(iterator, 0);
    StreamSupport.stream(spliterator, false).forEach(alignmentContext -> {
        final SimpleInterval alignmentInterval = new SimpleInterval(alignmentContext);
        apply(alignmentContext, new ReferenceContext(reference, alignmentInterval), new FeatureContext(features, alignmentInterval));
        progressMeter.update(alignmentInterval);
    });
    logger.info(countedFilter.getSummaryLine());
}

Example 15 with SAMFileHeader

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

the class ReplaceSamHeader method doWork.

/**
     * Do the work after command line has been parsed.
     * RuntimeException may be thrown by this method, and are reported appropriately.
     *
     * @return program exit status.
     */
@Override
protected Object doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsReadable(HEADER);
    IOUtil.assertFileIsWritable(OUTPUT);
    final SAMFileHeader replacementHeader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).getFileHeader(HEADER);
    if (BamFileIoUtils.isBamFile(INPUT)) {
        blockCopyReheader(replacementHeader);
    } else {
        standardReheader(replacementHeader);
    }
    return null;
}