Examples of SAMSequenceRecord

Examples of htsjdk.samtools.SAMSequenceRecord

                                                              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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Examples of htsjdk.samtools.SAMSequenceRecord

                                                             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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Examples of htsjdk.samtools.SAMSequenceRecord


    /**
     * 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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Examples of htsjdk.samtools.SAMSequenceRecord

    }


    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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Examples of htsjdk.samtools.SAMSequenceRecord


        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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Examples of htsjdk.samtools.SAMSequenceRecord

            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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Examples of htsjdk.samtools.SAMSequenceRecord

        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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Examples of htsjdk.samtools.SAMSequenceRecord

    }


    @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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Examples of net.sf.samtools.SAMSequenceRecord

                new BufferedInputStream(fis));
            BufferedInputStream bis = new BufferedInputStream(gis);
            List<CramIndex.Entry> full = CramIndex.readIndex(gis);


            List<CramIndex.Entry> entries = new LinkedList<CramIndex.Entry>();
            SAMSequenceRecord sequence = reader.getFileHeader()
                .getSequence(query.sequence);
            if (sequence == null)
              throw new RuntimeException("Sequence not found: "
                  + query.sequence);


            entries.addAll(CramIndex.find(full,
                sequence.getSequenceIndex(), query.start,
                query.end - query.start));


            bis.close();


            SAMIterator it = new SAMIterator(is, refFile);

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Examples of net.sf.samtools.SAMSequenceRecord

      int candidateIndex = getIndexOfMinAlignment();
      if (candidateIndex < 0) {
        next = null;
      } else {
        next = records[candidateIndex];
        SAMSequenceRecord sequence = header.getSequence(next
            .getReferenceName());


        next.setHeader(header);


        next.setReferenceIndex(sequence.getSequenceIndex());


        next.setReadName(sources[candidateIndex].id + delim
            + next.getReadName());


        if (next.getMateReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
          next.setMateAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
        } else {
          SAMSequenceRecord mateSequence = header.getSequence(next
              .getMateReferenceName());
          next.setMateReferenceIndex(mateSequence.getSequenceIndex());
        }


        if (sources[candidateIndex].it.hasNext())
          records[candidateIndex] = sources[candidateIndex].it.next();
        else

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