Examples with SAMSequenceDictionaryProgress com.github.lindenb.jvarkit.util.picard.SAMSequenceDictionaryProgress used on opensource projects

Example 56 with SAMSequenceDictionaryProgress

use of com.github.lindenb.jvarkit.util.picard.SAMSequenceDictionaryProgress in project jvarkit by lindenb.

the class SamFindClippedRegions method doWork.

/*private static boolean closeTo(int pos1,int pos2, int max)
		{
		return Math.abs(pos2-pos1)<=max;
		}*/
/*
	private static boolean same(char c1,char c2)
		{
		if(c1=='N' || c2=='N') return false;
		return Character.toUpperCase(c1)==Character.toUpperCase(c2);
		}*/
@Override
public int doWork(List<String> args) {
    int readLength = 150;
    if (args.isEmpty()) {
        LOG.error("illegal.number.of.arguments");
        return -1;
    }
    List<Input> inputs = new ArrayList<Input>();
    VariantContextWriter w = null;
    // SAMFileWriter w=null;
    try {
        SAMSequenceDictionary dict = null;
        /* create input, collect sample names */
        Map<String, Input> sample2input = new HashMap<String, Input>();
        for (final String filename : args) {
            Input input = new Input(new File(filename));
            // input.index=inputs.size();
            inputs.add(input);
            if (sample2input.containsKey(input.sampleName)) {
                LOG.error("Duplicate sample " + input.sampleName + " in " + input.bamFile + " and " + sample2input.get(input.sampleName).bamFile);
                return -1;
            }
            sample2input.put(input.sampleName, input);
            if (dict == null) {
                dict = input.header.getSequenceDictionary();
            } else if (!SequenceUtil.areSequenceDictionariesEqual(dict, input.header.getSequenceDictionary())) {
                LOG.error("Found more than one dictint sequence dictionary");
                return -1;
            }
        }
        LOG.info("Sample N= " + sample2input.size());
        /* create merged iterator */
        List<SAMFileHeader> headers = new ArrayList<SAMFileHeader>(sample2input.size());
        for (Input input : inputs) headers.add(input.header);
        SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(SortOrder.coordinate, headers, true);
        List<SamReader> readers = new ArrayList<SamReader>(sample2input.size());
        for (Input input : inputs) readers.add(input.samFileReaderScan);
        MergingSamRecordIterator merginIter = new MergingSamRecordIterator(headerMerger, readers, true);
        Allele reference_allele = Allele.create("N", true);
        Allele[] alternate_alleles = new Allele[] { Allele.create("<CLIP5>", false), Allele.create("<CLIP3>", false) };
        Set<VCFHeaderLine> vcfHeaderLines = new HashSet<VCFHeaderLine>();
        for (Allele alt : alternate_alleles) {
            vcfHeaderLines.add(new VCFSimpleHeaderLine("<ID=" + alt.getDisplayString() + ",Description=\"StructVar\">", VCFHeaderVersion.VCF4_1, VCFConstants.ALT_HEADER_START.substring(2), Arrays.asList("ID", "Description")));
        }
        vcfHeaderLines.add(new VCFInfoHeaderLine("COUNT_SAMPLES", 1, VCFHeaderLineType.Integer, "Number of samples with  depth>=" + this.min_depth));
        vcfHeaderLines.add(new VCFInfoHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Approximate read depth."));
        vcfHeaderLines.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
        vcfHeaderLines.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Approximate read depth"));
        vcfHeaderLines.add(new VCFHeaderLine(getClass().getSimpleName() + "CmdLine", String.valueOf(getProgramCommandLine())));
        vcfHeaderLines.add(new VCFHeaderLine(getClass().getSimpleName() + "Version", String.valueOf(getVersion())));
        for (int side = 0; side < 2; ++side) {
            vcfHeaderLines.add(new VCFFormatHeaderLine("CN" + (side == 0 ? 5 : 3), 1, VCFHeaderLineType.Integer, "count clipped in " + (side == 0 ? 5 : 3) + "'"));
        }
        if (dict != null) {
            vcfHeaderLines.addAll(VCFUtils.samSequenceDictToVCFContigHeaderLine(dict));
        }
        VCFHeader vcfHeader = new VCFHeader(vcfHeaderLines, sample2input.keySet());
        w = VCFUtils.createVariantContextWriterToStdout();
        w.writeHeader(vcfHeader);
        final IntervalTreeMap<Boolean> intervals = new IntervalTreeMap<>();
        // w=swf.make(header, System.out);
        SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(dict);
        if (bedFile != null) {
            final BedLineCodec bedLineCodec = new BedLineCodec();
            LOG.info("Reading " + bedFile);
            BufferedReader r = IOUtils.openFileForBufferedReading(bedFile);
            String line;
            while ((line = r.readLine()) != null) {
                BedLine bedLine = bedLineCodec.decode(line);
                if (bedLine == null)
                    continue;
                if (dict != null && dict.getSequence(bedLine.getContig()) == null) {
                    LOG.warning("undefined chromosome  in " + bedFile + " " + line);
                    continue;
                }
                intervals.put(bedLine.toInterval(), true);
            }
            CloserUtil.close(r);
        }
        LinkedList<SAMRecord> buffer = new LinkedList<SAMRecord>();
        final Predicate<SAMRecord> filterSamRecords = new Predicate<SAMRecord>() {

            @Override
            public boolean test(SAMRecord rec) {
                if (rec.getReadUnmappedFlag())
                    return false;
                if (rec.isSecondaryOrSupplementary())
                    return false;
                if (rec.getDuplicateReadFlag())
                    return false;
                if (rec.getReadFailsVendorQualityCheckFlag())
                    return false;
                Cigar cigar = rec.getCigar();
                if (cigar == null || cigar.numCigarElements() < 2)
                    return false;
                boolean found_S = false;
                for (int side = 0; side < 2; ++side) {
                    CigarElement ce = cigar.getCigarElement(side == 0 ? 0 : cigar.numCigarElements() - 1);
                    // read must be clipped on 5' or 3' with a good length
                    if (!ce.getOperator().equals(CigarOperator.S))
                        continue;
                    found_S = true;
                    break;
                }
                if (!found_S)
                    return false;
                SAMReadGroupRecord g = rec.getReadGroup();
                if (g == null || g.getSample() == null || g.getSample().isEmpty())
                    return false;
                return true;
            }
        };
        final FilteringIterator<SAMRecord> forwardIterator = new FilteringIterator<SAMRecord>(merginIter, filterSamRecords);
        for (; ; ) {
            SAMRecord rec = null;
            if (forwardIterator.hasNext()) {
                rec = forwardIterator.next();
                progress.watch(rec);
                if (intervals != null && !intervals.containsOverlapping(new Interval(rec.getReferenceName(), rec.getAlignmentStart(), rec.getAlignmentEnd())))
                    continue;
            }
            // need to flush buffer ?
            if (rec == null || (!buffer.isEmpty() && !buffer.getLast().getReferenceIndex().equals(rec.getReferenceIndex())) || (!buffer.isEmpty() && buffer.getLast().getUnclippedEnd() + readLength < rec.getUnclippedStart())) {
                if (!buffer.isEmpty()) {
                    int chromStart = buffer.getFirst().getUnclippedStart();
                    int chromEnd = buffer.getFirst().getUnclippedEnd();
                    for (SAMRecord sam : buffer) {
                        chromStart = Math.min(chromStart, sam.getUnclippedStart());
                        chromEnd = Math.max(chromEnd, sam.getUnclippedEnd());
                    }
                    final int winShift = 5;
                    for (int pos = chromStart; pos + winShift <= chromEnd; pos += winShift) {
                        int[] count_big_clip = new int[] { 0, 0 };
                        // int max_depth[]=new int[]{0,0};
                        List<Genotype> genotypes = new ArrayList<Genotype>();
                        Set<Allele> all_alleles = new HashSet<Allele>();
                        all_alleles.add(reference_allele);
                        boolean found_one_depth_ok = false;
                        int sum_depth = 0;
                        int samples_with_high_depth = 0;
                        for (String sample : sample2input.keySet()) {
                            GenotypeBuilder gb = new GenotypeBuilder(sample);
                            int[] count_clipped = new int[] { 0, 0 };
                            Set<Allele> sample_alleles = new HashSet<Allele>(3);
                            for (int side = 0; side < 2; ++side) {
                                for (SAMRecord sam : buffer) {
                                    if (!sam.getReadGroup().getSample().equals(sample))
                                        continue;
                                    Cigar cigar = sam.getCigar();
                                    CigarElement ce = cigar.getCigarElement(side == 0 ? 0 : cigar.numCigarElements() - 1);
                                    if (!ce.getOperator().equals(CigarOperator.S))
                                        continue;
                                    int clipStart = (side == 0 ? sam.getUnclippedStart() : sam.getAlignmentEnd() + 1);
                                    int clipEnd = (side == 0 ? sam.getAlignmentStart() - 1 : sam.getUnclippedEnd());
                                    if ((pos + winShift < clipStart || pos > clipEnd))
                                        continue;
                                    count_clipped[side]++;
                                    if (ce.getLength() >= this.min_clip_length) {
                                        count_big_clip[side]++;
                                    }
                                    sample_alleles.add(alternate_alleles[side]);
                                    gb.attribute("CN" + (side == 0 ? 5 : 3), count_clipped[side]);
                                }
                            }
                            // if(!(found_one_big_clip[0] || found_one_big_clip[1])) continue;
                            if (count_clipped[0] + count_clipped[1] == 0)
                                continue;
                            if ((count_clipped[0] + count_clipped[1]) > min_depth) {
                                found_one_depth_ok = true;
                                ++samples_with_high_depth;
                            }
                            sum_depth += (count_clipped[0] + count_clipped[1]);
                            gb.alleles(new ArrayList<Allele>(sample_alleles));
                            all_alleles.addAll(sample_alleles);
                            gb.DP(count_clipped[0] + count_clipped[1]);
                            genotypes.add(gb.make());
                        }
                        if (all_alleles.size() == 1) {
                            // all homozygotes
                            continue;
                        }
                        if (!found_one_depth_ok) {
                            continue;
                        }
                        if (!(count_big_clip[0] >= 1 || count_big_clip[1] >= 1)) {
                            continue;
                        }
                        Map<String, Object> atts = new HashMap<String, Object>();
                        atts.put("COUNT_SAMPLES", samples_with_high_depth);
                        atts.put(VCFConstants.DEPTH_KEY, sum_depth);
                        VariantContextBuilder vcb = new VariantContextBuilder();
                        vcb.chr(buffer.getFirst().getReferenceName());
                        vcb.start(pos);
                        vcb.stop(pos + winShift);
                        vcb.alleles(all_alleles);
                        vcb.attributes(atts);
                        vcb.genotypes(genotypes);
                        w.add(vcb.make());
                    }
                    buffer.clear();
                }
                if (rec == null) {
                    break;
                }
            }
            buffer.add(rec);
        }
        merginIter.close();
        progress.finish();
        return 0;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        for (Input input : inputs) {
            CloserUtil.close(input);
        }
    }
}

Example 57 with SAMSequenceDictionaryProgress

use of com.github.lindenb.jvarkit.util.picard.SAMSequenceDictionaryProgress in project jvarkit by lindenb.

the class SamSlop method doWork.

@Override
public int doWork(List<String> args) {
    if (this.faidx == null) {
        LOG.error("Reference was not specified.");
        return -1;
    }
    if (this.defaultQual.length() != 1) {
        LOG.error("default quality should have length==1 " + this.defaultQual);
    }
    GenomicSequence genomicSequence = null;
    SamReader sfr = null;
    SAMFileWriter sfw = null;
    IndexedFastaSequenceFile indexedFastaSequenceFile = null;
    final char defaultQUAL = this.defaultQual.charAt(0);
    try {
        final String inputName = oneFileOrNull(args);
        LOG.info("Loading reference");
        indexedFastaSequenceFile = new IndexedFastaSequenceFile(faidx);
        sfr = openSamReader(inputName);
        final SAMFileHeader header = sfr.getFileHeader();
        header.setSortOrder(SortOrder.unsorted);
        sfw = writingBamArgs.openSAMFileWriter(outputFile, header, true);
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header);
        final SAMRecordIterator iter = sfr.iterator();
        while (iter.hasNext()) {
            final SAMRecord rec = progress.watch(iter.next());
            final Cigar cigar = rec.getCigar();
            if (rec.getReadUnmappedFlag() || cigar == null || cigar.isEmpty() || rec.getReadBases() == SAMRecord.NULL_SEQUENCE || (this.extend5 <= 0 && this.extend3 <= 0)) {
                sfw.addAlignment(rec);
                continue;
            }
            final StringBuilder sbs = new StringBuilder(rec.getReadString());
            final StringBuilder sbq = new StringBuilder(rec.getBaseQualityString());
            if (genomicSequence == null || genomicSequence.getSAMSequenceRecord().getSequenceIndex() != rec.getReferenceIndex()) {
                genomicSequence = new GenomicSequence(indexedFastaSequenceFile, rec.getReferenceName());
            }
            final int refPos1 = (this.removeClip ? rec.getAlignmentStart() : rec.getUnclippedStart());
            final int endAlignmend1 = (this.removeClip ? rec.getAlignmentEnd() : rec.getUnclippedEnd());
            final List<CigarElement> cl = new ArrayList<>(cigar.getCigarElements());
            if (!this.removeClip) {
                // replace clip S/H by match M
                for (int i = 0; i < cl.size(); ++i) {
                    final CigarElement ce = cl.get(i);
                    if (ce.getOperator() == CigarOperator.S || ce.getOperator() == CigarOperator.H) {
                        cl.set(i, new CigarElement(ce.getLength(), CigarOperator.M));
                    }
                }
            }
            if (this.extend5 > 0 && refPos1 > 1) {
                if (this.removeClip) {
                    // /remove hard + soft clip 5'
                    while (!cl.isEmpty()) {
                        // first
                        final CigarElement ce = cl.get(0);
                        // not a clip
                        if (!(ce.getOperator() == CigarOperator.S || ce.getOperator() == CigarOperator.H)) {
                            break;
                        }
                        if (ce.getOperator() == CigarOperator.S) {
                            sbs.replace(0, ce.getLength(), "");
                            sbq.replace(0, ce.getLength(), "");
                        }
                        // remove first
                        cl.remove(0);
                    }
                }
                final StringBuilder prefix = new StringBuilder(this.extend5);
                // /append + soft clip 5'
                for (int i = 0; i < this.extend5; ++i) {
                    int x1 = (refPos1 - 1) - i;
                    // break if out of genome
                    if (x1 < 1)
                        break;
                    prefix.insert(0, genomicSequence.charAt(x1 - 1));
                }
                sbs.insert(0, prefix.toString());
                // preprend quality
                for (int i = 0; i < prefix.length(); ++i) sbq.insert(0, defaultQUAL);
                // prepend cigar
                cl.add(0, new CigarElement(prefix.length(), CigarOperator.M));
                // update start pos
                rec.setAlignmentStart(refPos1 - prefix.length());
            }
            if (this.extend3 > 0 && rec.getAlignmentEnd() < genomicSequence.length()) {
                if (this.removeClip) {
                    // /remove hard + soft clip 3'
                    while (!cl.isEmpty()) {
                        // last
                        final CigarElement ce = cl.get(cl.size() - 1);
                        // not a clip
                        if (!(ce.getOperator() == CigarOperator.S || ce.getOperator() == CigarOperator.H)) {
                            break;
                        }
                        if (ce.getOperator() == CigarOperator.S) {
                            sbs.setLength(sbs.length() - ce.getLength());
                            sbq.setLength(sbq.length() - ce.getLength());
                        }
                        // remove last
                        cl.remove(cl.size() - 1);
                    }
                }
                int extend = 0;
                for (int pos1 = endAlignmend1 + 1; pos1 <= (endAlignmend1 + this.extend3) && pos1 <= genomicSequence.length(); ++pos1) {
                    sbs.append(genomicSequence.charAt(pos1 - 1));
                    sbq.append(defaultQUAL);
                    ++extend;
                }
                // append cigar
                cl.add(new CigarElement(extend, CigarOperator.M));
            }
            // simplify cigar
            int idx = 0;
            while (idx + 1 < cl.size()) {
                final CigarElement ce1 = cl.get(idx);
                final CigarElement ce2 = cl.get(idx + 1);
                if (ce1.getOperator() == ce2.getOperator()) {
                    cl.set(idx, new CigarElement(ce1.getLength() + ce2.getLength(), ce1.getOperator()));
                    cl.remove(idx + 1);
                } else {
                    idx++;
                }
            }
            rec.setCigar(new Cigar(cl));
            rec.setReadString(sbs.toString());
            rec.setBaseQualityString(sbq.toString());
            final List<SAMValidationError> errors = rec.isValid();
            if (errors != null && !errors.isEmpty()) {
                for (SAMValidationError err : errors) {
                    LOG.error(err.getMessage());
                }
            }
            // info("changed "+rec.getCigarString()+" to "+newCigarStr+" "+rec.getReadName()+" "+rec.getReadString());
            sfw.addAlignment(rec);
        }
        progress.finish();
        return RETURN_OK;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(indexedFastaSequenceFile);
        CloserUtil.close(sfr);
        CloserUtil.close(sfw);
    }
}

Example 58 with SAMSequenceDictionaryProgress

use of com.github.lindenb.jvarkit.util.picard.SAMSequenceDictionaryProgress in project jvarkit by lindenb.

the class SortSamRefName method doWork.

@Override
public int doWork(List<String> args) {
    SamReader in = null;
    SAMFileWriter out = null;
    SAMRecordIterator iter = null;
    CloseableIterator<SAMRecord> iter2 = null;
    SortingCollection<SAMRecord> sorter = null;
    try {
        in = openSamReader(oneFileOrNull(args));
        final SAMFileHeader header = in.getFileHeader();
        final BAMRecordCodec bamRecordCodec = new BAMRecordCodec(header);
        final RefNameComparator refNameComparator = new RefNameComparator();
        sorter = SortingCollection.newInstance(SAMRecord.class, bamRecordCodec, refNameComparator, this.writingSortingCollection.getMaxRecordsInRam(), this.writingSortingCollection.getTmpPaths());
        sorter.setDestructiveIteration(true);
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header);
        iter = in.iterator();
        while (iter.hasNext()) {
            sorter.add(progress.watch(iter.next()));
        }
        in.close();
        in = null;
        sorter.doneAdding();
        final SAMFileHeader header2 = header.clone();
        header2.addComment(getProgramName() + " " + getVersion() + " " + getProgramCommandLine());
        header2.setSortOrder(SortOrder.unsorted);
        out = this.writingBamArgs.openSAMFileWriter(outputFile, header2, true);
        iter2 = sorter.iterator();
        while (iter2.hasNext()) {
            out.addAlignment(iter2.next());
        }
        out.close();
        out = null;
        sorter.cleanup();
        progress.finish();
        LOG.info("done");
        return RETURN_OK;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(iter2);
        CloserUtil.close(iter);
        CloserUtil.close(out);
        CloserUtil.close(in);
    }
}

Example 59 with SAMSequenceDictionaryProgress

use of com.github.lindenb.jvarkit.util.picard.SAMSequenceDictionaryProgress in project jvarkit by lindenb.

the class SplitVcf method doWork.

private int doWork(final String inputName) {
    if (this.outputFile == null || !this.outputFile.getName().contains(REPLACE_GROUPID)) {
        throw new JvarkitException.UserError("Output file pattern undefined or doesn't contain " + REPLACE_GROUPID + " : " + this.outputFile);
    }
    if (!(this.outputFile.getName().endsWith(".vcf") || this.outputFile.getName().endsWith(".vcf.gz"))) {
        throw new JvarkitException.UserError("output file must end with '.vcf' or '.vcf.gz'");
    }
    BufferedReader r = null;
    VcfIterator in = null;
    try {
        in = openVcfIterator(inputName);
        final SAMSequenceDictionary samSequenceDictionary = in.getHeader().getSequenceDictionary();
        if (samSequenceDictionary == null) {
            throw new JvarkitException.VcfDictionaryMissing(inputName == null ? "<input>" : inputName);
        }
        this.underminedGroup = new SplitGroup(UNDERTERMINED_NAME);
        this.name2group.put(UNDERTERMINED_NAME, this.underminedGroup);
        if (this.chromGroupFile != null) {
            r = IOUtils.openFileForBufferedReading(this.chromGroupFile);
            String line;
            while ((line = r.readLine()) != null) {
                if (line.isEmpty() || line.startsWith("#"))
                    continue;
                final String[] tokens = line.split("[ \t,]+");
                final String groupName = tokens[0].trim();
                if (groupName.isEmpty())
                    throw new JvarkitException.UserError("Empty group name in " + line);
                if (this.UNDERTERMINED_NAME.equals(groupName))
                    throw new JvarkitException.UserError("Group cannot be named " + UNDERTERMINED_NAME);
                if (this.name2group.containsKey(groupName))
                    throw new JvarkitException.UserError("Group defined twice " + groupName);
                for (int i = 1; i < tokens.length; i++) {
                    String sequence;
                    int start;
                    int end;
                    final String segment = tokens[i].trim();
                    if (segment.isEmpty())
                        continue;
                    int colon = segment.indexOf(':');
                    if (colon == -1) {
                        final SAMSequenceRecord ssr = samSequenceDictionary.getSequence(segment);
                        if (ssr == null) {
                            throw new JvarkitException.ContigNotFoundInDictionary(segment, samSequenceDictionary);
                        }
                        sequence = segment;
                        start = 1;
                        end = ssr.getSequenceLength();
                    } else {
                        int hyphen = segment.indexOf('-', colon);
                        if (hyphen == -1)
                            throw new JvarkitException.UserError("Bad segment:" + segment);
                        sequence = segment.substring(0, colon);
                        if (samSequenceDictionary.getSequence(sequence) == null)
                            throw new JvarkitException.UserError("Unknown chromosome , not in dict " + segment);
                        start = Integer.parseInt(segment.substring(colon + 1, hyphen));
                        end = Integer.parseInt(segment.substring(hyphen + 1));
                    }
                    final Interval interval = new Interval(sequence, start, end);
                    this.putInterval(groupName, interval);
                }
            }
            r.close();
            r = null;
        } else {
            LOG.info("creating default split interval");
            for (final SAMSequenceRecord seq : samSequenceDictionary.getSequences()) {
                final String groupName = seq.getSequenceName();
                final Interval interval = new Interval(groupName, 1, seq.getSequenceLength());
                this.putInterval(groupName, interval);
            }
        }
        /* open all output vcf */
        for (final SplitGroup g : this.name2group.values()) {
            g.open(in.getHeader());
        }
        /* loop over vcf variations */
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(samSequenceDictionary);
        while (in.hasNext()) {
            final VariantContext record = progress.watch(in.next());
            final Interval interval = new Interval(record.getContig(), record.getStart(), record.getEnd());
            Set<SplitGroup> splitGroups = this.getGroupsFromInterval(interval);
            if (splitGroups.isEmpty()) {
                splitGroups = Collections.singleton(this.underminedGroup);
            }
            for (final SplitGroup splitGroup : splitGroups) {
                splitGroup._writer.add(record);
            }
        }
        progress.finish();
        in.close();
        for (final SplitGroup g : this.name2group.values()) {
            g.close();
        }
        return 0;
    } catch (final Exception err) {
        for (final SplitGroup g : this.name2group.values()) {
            CloserUtil.close(g);
            if (in != null)
                g.getFile().delete();
        }
        return -1;
    } finally {
        for (final SplitGroup g : this.name2group.values()) {
            CloserUtil.close(g);
        }
        CloserUtil.close(r);
        CloserUtil.close(in);
        this.name2group.clear();
        this.interval2group.clear();
    }
}

Example 60 with SAMSequenceDictionaryProgress

use of com.github.lindenb.jvarkit.util.picard.SAMSequenceDictionaryProgress in project jvarkit by lindenb.

the class VCFPolyX method doVcfToVcf.

@Override
protected int doVcfToVcf(final String inputName, final VcfIterator r, final VariantContextWriter delegate) {
    final VariantContextWriter w = this.component.open(delegate);
    w.writeHeader(r.getHeader());
    final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(r.getHeader()).logger(LOG);
    while (r.hasNext()) {
        w.add(progress.watch(r.next()));
    }
    progress.finish();
    w.close();
    return RETURN_OK;
}