Examples with BwaMemAlignment org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment used on opensource projects

Example 1 with BwaMemAlignment

use of org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment in project gatk by broadinstitute.

the class AlignedAssemblyOrExcuse method toSAMStreamForOneContig.

public static Stream<SAMRecord> toSAMStreamForOneContig(final SAMFileHeader header, final List<String> refNames, final int assemblyId, final int contigIdx, final byte[] contigSequence, final List<BwaMemAlignment> alignments) {
    if (alignments.isEmpty())
        return Stream.empty();
    final String readName = formatContigName(assemblyId, contigIdx);
    final Map<BwaMemAlignment, String> saTagMap = BwaMemAlignmentUtils.createSATags(alignments, refNames);
    return alignments.stream().map(alignment -> {
        final SAMRecord samRecord = BwaMemAlignmentUtils.applyAlignment(readName, contigSequence, null, null, alignment, refNames, header, false, false);
        final String saTag = saTagMap.get(alignment);
        if (saTag != null)
            samRecord.setAttribute("SA", saTag);
        return samRecord;
    });
}

Example 2 with BwaMemAlignment

use of org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment in project gatk by broadinstitute.

the class BwaMemTestUtils method assertCorrectSingleReadAlignment.

public static void assertCorrectSingleReadAlignment(final BwaMemIndex index) {
    try (final BwaMemAligner aligner = new BwaMemAligner(index)) {
        //real read taken from src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam
        final byte[] seq = "GTTTTGTTTACTACAGCTTTGTAGTAAATTTTGAACTCTAAAGTGTTAGTTCTCTAACTTTGTTTGTTTTTCAAGAGTGTTTTGACTCTTCTTACTGCATC".getBytes();
        final List<List<BwaMemAlignment>> allAlignments = aligner.alignSeqs(Collections.singletonList(seq));
        Assert.assertEquals(allAlignments.size(), 1);
        final List<BwaMemAlignment> alignments = allAlignments.get(0);
        Assert.assertEquals(alignments.size(), 1);
        final BwaMemAlignment alignment = alignments.get(0);
        Assert.assertEquals(index.getReferenceContigNames().get(alignment.getRefId()), "20");
        Assert.assertEquals(alignment.getCigar(), "101M");
        Assert.assertEquals(alignment.getMapQual(), 60);
        Assert.assertEquals(alignment.getRefStart(), 9999996);
        Assert.assertEquals(alignment.getNMismatches(), 0);
    }
}

Example 3 with BwaMemAlignment

use of org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment in project gatk by broadinstitute.

the class AlignedAssemblyUnitTest method createInputsAndExpectedResults_BwaMemAlignmentConstruction.

/**
     * These alignment records are supposed to be associated with the 4 possible types of evidence we could see for an inversion,
     *   where the chr1:101-200 bases are inverted, namely
     * INV55, where lower  contig coordinate is associated with a forward  strand lower reference coordinate, and
     *              higher contig coordinate is associated with a negative strand higher reference/contig coordinate
     * INV55, where lower  contig coordinate is associated with a forward  strand higher reference coordinate, and
     *              higher contig coordinate is associated with a negative strand lower reference/contig coordinate
     * INV33, where lower  contig coordinate is associated with a negative strand lower reference coordinate, and
     *              higher contig coordinate is associated with a forward  strand higher reference/contig coordinate
     * INV33, where lower  contig coordinate is associated with a forward  strand higher reference coordinate, and
     *              higher contig coordinate is associated with a negative strand lower reference/contig coordinate
     * Finally, one must be aware of the fact that BWA always outputs CIGAR with a '+'-strand representation,
     *   therefore we must use such in constructing the BwaMemAlignment's* @return objects stored in each array
     * @return an array of arrays, each composed of
     * [0] {@link BwaMemAlignment} object,
     * [1] expected reference interval,
     * [2] expected cigar,
     * [3] expected strandedness,
     * [4] expected start in assembled contig, 1-based, inclusive
     * [5] expected end in assembled contig, 1-based, inclusive
     * [6] expected contig length,
     * [7] expected {@link AlignedAssembly.AlignmentInterval} object (generated manually with all fields explicitly spell out and given to
     *                                      {@link AlignedAssembly.AlignmentInterval#AlignmentInterval(SimpleInterval, int, int, Cigar, boolean, int, int)}
     *                                      intended to be used for testing concordance between the two constructors)
     */
@DataProvider(name = "AlignmentIntervalCtorTestForSimpleInversion")
private Object[][] createInputsAndExpectedResults_BwaMemAlignmentConstruction() {
    final int[] alignmentStartsOnRef_0Based = { 96, 196, 195, 95, 101, 201, 101, 201 };
    final int[] alignmentStartsOnTig_0BasedInclusive = { 0, 4, 0, 5, 0, 6, 0, 7 };
    final int[] alignmentEndsOnTig_0BasedExclusive = { 4, 8, 5, 10, 6, 12, 7, 14 };
    final int[] seqLen = { 8, 8, 10, 10, 12, 12, 14, 14 };
    final int[] mapQualForBwaMemAlgn = { -1, 0, 10, 20, 30, 40, 50, 60 };
    final boolean[] strandedness = { true, false, true, false, false, true, false, true };
    // each different number represent a different contig's pair of chimeric alignments
    final String[] cigarStrings = { "4M4S", "4M4H", "5M5S", "5M5H", "6S6M", "6H6M", "7S7M", "7H7M" };
    final Cigar[] cigars = Arrays.stream(cigarStrings).map(TextCigarCodec::decode).toArray(Cigar[]::new);
    final Object[][] data = new Object[cigars.length][];
    for (int i = 0; i < cigars.length; ++i) {
        final BwaMemAlignment bwaMemAlignment = new BwaMemAlignment(strandedness[i] ? 0 : SAMFlag.READ_REVERSE_STRAND.intValue(), 0, alignmentStartsOnRef_0Based[i], alignmentStartsOnRef_0Based[i] + cigars[i].getReferenceLength(), strandedness[i] ? alignmentStartsOnTig_0BasedInclusive[i] : seqLen[i] - alignmentEndsOnTig_0BasedExclusive[i], strandedness[i] ? alignmentEndsOnTig_0BasedExclusive[i] : seqLen[i] - alignmentStartsOnTig_0BasedInclusive[i], mapQualForBwaMemAlgn[i], 0, 1, 1, cigarStrings[i], null, null, 0, Integer.MIN_VALUE, Integer.MAX_VALUE);
        final SimpleInterval referenceInterval = new SimpleInterval(refNames.get(0), alignmentStartsOnRef_0Based[i] + 1, bwaMemAlignment.getRefEnd());
        final AlignedAssembly.AlignmentInterval alignmentInterval = new AlignedAssembly.AlignmentInterval(referenceInterval, alignmentStartsOnTig_0BasedInclusive[i] + 1, alignmentEndsOnTig_0BasedExclusive[i], strandedness[i] ? cigars[i] : CigarUtils.invertCigar(cigars[i]), strandedness[i], Math.max(SAMRecord.NO_MAPPING_QUALITY, bwaMemAlignment.getMapQual()), bwaMemAlignment.getNMismatches());
        data[i] = new Object[] { bwaMemAlignment, referenceInterval, strandedness[i] ? cigars[i] : CigarUtils.invertCigar(cigars[i]), strandedness[i], alignmentStartsOnTig_0BasedInclusive[i] + 1, alignmentEndsOnTig_0BasedExclusive[i], seqLen[i], mapQualForBwaMemAlgn[i], alignmentInterval };
    }
    return data;
}

Example 4 with BwaMemAlignment

use of org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment in project gatk by broadinstitute.

the class AlignedAssemblyOrExcuse method serialize.

private void serialize(final Kryo kryo, final Output output) {
    output.writeInt(assemblyId);
    output.writeString(errorMessage);
    if (errorMessage == null) {
        final int nContigs = assembly.getNContigs();
        final Map<Contig, Integer> contigMap = new HashMap<>();
        output.writeInt(nContigs);
        for (int idx = 0; idx != nContigs; ++idx) {
            final Contig contig = assembly.getContig(idx);
            writeContig(contig, output);
            contigMap.put(contig, idx);
        }
        for (final Contig contig : assembly.getContigs()) {
            final List<Connection> connections = contig.getConnections();
            output.writeInt(connections.size());
            for (final Connection connection : connections) {
                writeConnection(connection, contigMap, output);
            }
        }
        for (final List<BwaMemAlignment> alignments : contigAlignments) {
            output.writeInt(alignments.size());
            for (final BwaMemAlignment alignment : alignments) {
                writeAlignment(alignment, output);
            }
        }
    }
}

Example 5 with BwaMemAlignment

use of org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment in project gatk by broadinstitute.

the class ContigAligner method alignContigs.

/**
     * Takes a collection of assembled contigs and aligns them to the reference with bwa-mem. Non-canonical
     * (secondary) alignments are filtered out, preserving the primary and supplementary alignments.
     * Within the output list, alignments are sorted first by contig (based on the order in which
     * the contigs were passed in, and then by their start position on the contig).
     * @param assemblyId An identifier for the assembly or set of contigs
     * @param contigsCollection The set of all canonical (primary or supplementary) alignments for the contigs.*/
AlignedAssembly alignContigs(final int assemblyId, final ContigsCollection contigsCollection) {
    final List<AlignedContig> alignedContigs = new ArrayList<>(contigsCollection.getContents().size());
    final BwaMemIndex index = BwaMemIndexSingleton.getInstance(indexImageFile);
    try (final BwaMemAligner aligner = new BwaMemAligner(index)) {
        final List<String> refNames = index.getReferenceContigNames();
        final List<Tuple2<ContigsCollection.ContigID, ContigsCollection.ContigSequence>> contents = contigsCollection.getContents();
        final List<byte[]> seqs = contents.stream().map(contigInfo -> contigInfo._2.toString().getBytes()).collect(Collectors.toList());
        final List<List<BwaMemAlignment>> allAlignments = aligner.alignSeqs(seqs);
        for (int contigIdx = 0; contigIdx < seqs.size(); ++contigIdx) {
            final int contigLen = seqs.get(contigIdx).length;
            // filter out secondary alignments, convert to AlignmentInterval objects and sort by alignment start pos
            final List<AlignedAssembly.AlignmentInterval> alignmentIntervals = allAlignments.get(contigIdx).stream().filter(a -> (a.getSamFlag() & SAMFlag.NOT_PRIMARY_ALIGNMENT.intValue()) == 0).filter(a -> (a.getSamFlag() & SAMFlag.READ_UNMAPPED.intValue()) == 0).map(a -> new AlignedAssembly.AlignmentInterval(a, refNames, contigLen)).sorted(Comparator.comparing(a -> a.startInAssembledContig)).collect(Collectors.toList());
            final String contigName = AlignedAssemblyOrExcuse.formatContigName(assemblyId, Integer.valueOf(contents.get(contigIdx)._1.toString().split(" ")[0].replace("contig", "").replace("-", "").replace(">", "")));
            alignedContigs.add(new AlignedContig(contigName, seqs.get(contigIdx), alignmentIntervals));
        }
    }
    return new AlignedAssembly(assemblyId, alignedContigs);
}