Package htsjdk.samtools

Examples of htsjdk.samtools.SAMSequenceRecord

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                                                              int alignmentEnd,
                                                              int readLength,
                                                              Cigar oldCigar) {
        Cigar newCigar = null;
        if (!isUnmapped) {
            final SAMSequenceRecord refseq = header.getSequence(referenceIndex);
            final int overhang = alignmentEnd - refseq.getSequenceLength();
            if (overhang > 0) {
                // 1-based index of first base in read to clip.
                int clipFrom = readLength - overhang + 1;
                // we have to check if the last element is soft-clipping, so we can subtract that from clipFrom
                final CigarElement cigarElement = oldCigar.getCigarElement(oldCigar.getCigarElements().size()-1);
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                                                             final SAMSequenceDictionary readsDict) {
        Map<Integer, Integer> newOrder = new HashMap<Integer, Integer>();

        log.info("Reordering SAM/BAM file:");
        for (final SAMSequenceRecord refRec : refDict.getSequences() ) {
            final SAMSequenceRecord readsRec = readsDict.getSequence(refRec.getSequenceName());

            if (readsRec != null) {
                if ( refRec.getSequenceLength() != readsRec.getSequenceLength() ) {
                    String msg = String.format("Discordant contig lengths: read %s LN=%d, ref %s LN=%d",
                            readsRec.getSequenceName(), readsRec.getSequenceLength(),
                            refRec.getSequenceName(), refRec.getSequenceLength());
                    if ( ALLOW_CONTIG_LENGTH_DISCORDANCE ) {
                        log.warn(msg);
                    }
                    else {
                        throw new PicardException(msg);
                    }
                }

                log.info(String.format("  Reordering read contig %s [index=%d] to => ref contig %s [index=%d]%n",
                                       readsRec.getSequenceName(), readsRec.getSequenceIndex(),
                                       refRec.getSequenceName(), refRec.getSequenceIndex()  ));
                newOrder.put(readsRec.getSequenceIndex(), refRec.getSequenceIndex());
            }
        }

        for ( SAMSequenceRecord readsRec : readsDict.getSequences() ) {
            if ( ! newOrder.containsKey(readsRec.getSequenceIndex()) ) {
                if ( ALLOW_INCOMPLETE_DICT_CONCORDANCE )
                    newOrder.put(readsRec.getSequenceIndex(), -1);
                else
                    throw new PicardException("New reference sequence does not contain a matching contig for " + readsRec.getSequenceName());
            }
        }

        return newOrder;
    }
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    /**
     * Create one SAMSequenceRecord from a single fasta sequence
     */
    private SAMSequenceRecord makeSequenceRecord(final ReferenceSequence refSeq) {
        final SAMSequenceRecord ret = new SAMSequenceRecord(refSeq.getName(), refSeq.length());

        // Compute MD5 of upcased bases
        final byte[] bases = refSeq.getBases();
        for (int i = 0; i < bases.length; ++i) {
                bases[i] = StringUtil.toUpperCase(bases[i]);
            }

        ret.setAttribute(SAMSequenceRecord.MD5_TAG, md5Hash(bases));
        if (GENOME_ASSEMBLY != null) {
            ret.setAttribute(SAMSequenceRecord.ASSEMBLY_TAG, GENOME_ASSEMBLY);
        }
        ret.setAttribute(SAMSequenceRecord.URI_TAG, URI);
        if (SPECIES != null) {
                ret.setAttribute(SAMSequenceRecord.SPECIES_TAG, SPECIES);
            }
        return ret;
    }
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    }

    public static HashSet<Integer> makeIgnoredSequenceIndicesSet(final SAMFileHeader header, final Set<String> ignoredSequence) {
        final HashSet<Integer> ignoredSequenceIndices = new HashSet<Integer>();
        for (final String sequenceName: ignoredSequence) {
            final SAMSequenceRecord sequenceRecord = header.getSequence(sequenceName);
            if (sequenceRecord == null) {
                throw new PicardException("Unrecognized sequence " + sequenceName + " passed as argument to IGNORE_SEQUENCE");
            }
            ignoredSequenceIndices.add(sequenceRecord.getSequenceIndex());
        }
        return ignoredSequenceIndices;
    }
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        final File alignedSam = File.createTempFile("aligned.", ".sam");
        alignedSam.deleteOnExit();

        // Populate the header with SAMSequenceRecords
        header.getSequenceDictionary().addSequence(new SAMSequenceRecord("chr1", 1000000));

        // Create 2 alignments for each end of pair
        final SAMFileWriter alignedWriter = factory.makeSAMWriter(header, false, alignedSam);
        for (int i = 1; i <= 2; ++i) {
            final SAMRecord firstOfPairAligned = new SAMRecord(header);
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            final File alignedSam = File.createTempFile("aligned.", ".sam");
            alignedSam.deleteOnExit();

            final String sequence = "chr1";
            // Populate the header with SAMSequenceRecords
            header.getSequenceDictionary().addSequence(new SAMSequenceRecord(sequence, 1000000));

            final SAMFileWriter alignedWriter = factory.makeSAMWriter(header, false, alignedSam);
            for (final MultipleAlignmentSpec spec : specs) {
                final SAMRecord alignedRecord = new SAMRecord(header);
                alignedRecord.setReadName(unmappedRecord.getReadName());
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        final File alignedSam = File.createTempFile("aligned.", ".sam");
        alignedSam.deleteOnExit();

        final String sequence = "chr1";
        // Populate the header with SAMSequenceRecords
        header.getSequenceDictionary().addSequence(new SAMSequenceRecord(sequence, 1000000));

        final SAMFileWriter alignedWriter = factory.makeSAMWriter(header, false, alignedSam);

        addAlignmentsForBestFragmentMapqStrategy(alignedWriter, firstUnmappedRead, sequence, firstMapQs);
        addAlignmentsForBestFragmentMapqStrategy(alignedWriter, secondUnmappedRead, sequence, secondMapQs);
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    }

    @Test(dataProvider = "testSegregate")
    public void testSegregateReference(final String referenceString, final int maxNmerToMerge, final List<Interval> result) throws Exception {

        final SAMSequenceRecord record = new SAMSequenceRecord("fake1", referenceString.length());
        final SAMSequenceDictionary dictionary = new SAMSequenceDictionary();
        dictionary.addSequence(record);

        final ReferenceSequenceFile reference = new ReferenceSequenceFile() {

            boolean done = false;

            @Override
            public SAMSequenceDictionary getSequenceDictionary() {
                return dictionary;
            }

            @Override
            public ReferenceSequence nextSequence() {
                if (!done) {
                    done = true;
                    return getSequence(record.getSequenceName());
                }
                return null;
            }

            @Override
            public void reset() {
                done = false;
            }

            @Override
            public boolean isIndexed() {
                return false;
            }

            @Override
            public ReferenceSequence getSequence(final String contig) {
                if (contig.equals(record.getSequenceName())) {
                    return new ReferenceSequence(record.getSequenceName(), 0, referenceString.getBytes());
                } else {
                    return null;
                }
            }
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Related Classes of htsjdk.samtools.SAMSequenceRecord

  • org.broad.igv.plugin.mongovariant.VariantReviewSource
  • org.broadinstitute.gatk.engine.alignment.bwa.BWTFiles
  • org.broadinstitute.gatk.engine.datasources.providers.ReferenceView
  • org.broadinstitute.gatk.engine.datasources.providers.ReferenceViewTemplate
  • org.broadinstitute.gatk.engine.datasources.reads.BAMScheduler
  • org.broadinstitute.gatk.engine.datasources.reads.IntervalOverlapFilteringIteratorUnitTest
  • org.broadinstitute.gatk.engine.iterators.VerifyingSamIteratorUnitTest
  • org.broadinstitute.gatk.engine.refdata.tracks.IndexDictionaryUtils
  • org.broadinstitute.gatk.tools.walkers.qc.CountRODs
  • org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile
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