Examples with VCFHeader htsjdk.variant.vcf.VCFHeader used on opensource projects

Example 76 with VCFHeader

use of htsjdk.variant.vcf.VCFHeader in project jvarkit by lindenb.

the class VariantContextBatchWriter method open.

@Override
public void open(final ExecutionContext executionContext) throws ItemStreamException {
    if (this.filenameFactory == null)
        throw new ItemStreamException("resource is not defined");
    try {
        final String filename = this.filenameFactory.apply(executionContext);
        if (StringUtil.isBlank(filename))
            throw new ItemStreamException("No output file defined.");
        if (LOG.isInfoEnabled())
            LOG.info("Opening " + filename + " for writing");
        if (!Arrays.stream(IOUtil.VCF_EXTENSIONS).anyMatch(SUFF -> filename.endsWith(SUFF))) {
            throw new ItemStreamException("Bad extension for a VCF file:" + filename);
        }
        final File vcfFile = new File(filename);
        VCFHeader header = SpringBatchUtils.getVcfHeader(executionContext);
        final VariantContextWriterBuilder vcwb = new VariantContextWriterBuilder();
        vcwb.setOutputFile(vcfFile);
        if (this.reference != null) {
            final SAMSequenceDictionary dic = SAMSequenceDictionaryExtractor.extractDictionary(this.reference);
            vcwb.setReferenceDictionary(dic);
            if (header.getSequenceDictionary() == null) {
                header = new VCFHeader(header);
                header.setSequenceDictionary(dic);
            }
        } else {
            vcwb.setReferenceDictionary(header.getSequenceDictionary());
        }
        vcwb.setCreateMD5(this.createMD5);
        this.vcw = vcwb.build();
        this.vcw.writeHeader(header);
    } catch (final Exception err) {
        priv_close();
        throw new ItemStreamException(err);
    }
}

Example 77 with VCFHeader

use of htsjdk.variant.vcf.VCFHeader in project jvarkit by lindenb.

the class IndexCovToVcf method doWork.

@Override
public int doWork(final List<String> args) {
    if (this.deletionTreshold >= 1.0f) {
        LOG.error("Bad deletion treshold >=1.0");
        return -1;
    }
    if (this.duplicationTreshold <= 1.0f) {
        LOG.error("Bad duplication treshold <=1.0");
        return -1;
    }
    if (this.deletionTreshold >= this.duplicationTreshold) {
        LOG.error("Bad tresholds del>=dup");
        return -1;
    }
    final Pattern tab = Pattern.compile("[\t]");
    BufferedReader r = null;
    VariantContextWriter vcw = null;
    try {
        final SAMSequenceDictionary dict;
        if (this.refFile == null) {
            dict = null;
        } else {
            dict = SAMSequenceDictionaryExtractor.extractDictionary(this.refFile);
            if (dict == null) {
                LOG.error("Cannot find dict in " + this.refFile);
                return -1;
            }
        }
        r = super.openBufferedReader(oneFileOrNull(args));
        String line = r.readLine();
        if (line == null) {
            LOG.error("Cannot read first line of input");
            return -1;
        }
        String[] tokens = tab.split(line);
        if (tokens.length < 4 || !tokens[0].equals("#chrom") || !tokens[1].equals("start") || !tokens[2].equals("end")) {
            LOG.error("bad first line " + line);
            return -1;
        }
        final Set<VCFHeaderLine> metaData = new HashSet<>();
        VCFStandardHeaderLines.addStandardFormatLines(metaData, true, "GT");
        VCFStandardHeaderLines.addStandardInfoLines(metaData, true, "END");
        final VCFFormatHeaderLine foldHeader = new VCFFormatHeaderLine("F", 1, VCFHeaderLineType.Float, "Relative number of copy: 0.5 deletion 1 normal 2.0 duplication");
        metaData.add(foldHeader);
        final VCFFormatHeaderLine formatIsDeletion = new VCFFormatHeaderLine("DEL", 1, VCFHeaderLineType.Integer, "set to 1 if relative number of copy <= " + this.deletionTreshold);
        metaData.add(formatIsDeletion);
        final VCFFormatHeaderLine formatIsDuplication = new VCFFormatHeaderLine("DUP", 1, VCFHeaderLineType.Integer, "set to 1 if relative number of copy >= " + this.duplicationTreshold);
        metaData.add(formatIsDuplication);
        final VCFFilterHeaderLine filterAllDel = new VCFFilterHeaderLine("ALL_DEL", "number of samples greater than 1 and all are deletions");
        metaData.add(filterAllDel);
        final VCFFilterHeaderLine filterAllDup = new VCFFilterHeaderLine("ALL_DUP", "number of samples  greater than  1 and all are duplication");
        metaData.add(filterAllDup);
        final VCFFilterHeaderLine filterNoSV = new VCFFilterHeaderLine("NO_SV", "There is no DUP or DEL in this variant");
        metaData.add(filterNoSV);
        final VCFInfoHeaderLine infoNumDup = new VCFInfoHeaderLine("NDUP", 1, VCFHeaderLineType.Integer, "Number of samples being duplicated");
        metaData.add(infoNumDup);
        final VCFInfoHeaderLine infoNumDel = new VCFInfoHeaderLine("NDEL", 1, VCFHeaderLineType.Integer, "Number of samples being deleted");
        metaData.add(infoNumDel);
        final List<String> samples = Arrays.asList(tokens).subList(3, tokens.length);
        final VCFHeader vcfHeader = new VCFHeader(metaData, samples);
        if (dict != null) {
            vcfHeader.setSequenceDictionary(dict);
        }
        vcw = super.openVariantContextWriter(outputFile);
        vcw.writeHeader(vcfHeader);
        // final List<Allele> NO_CALL_NO_CALL = Arrays.asList(Allele.NO_CALL,Allele.NO_CALL);
        final Allele DUP_ALLELE = Allele.create("<DUP>", false);
        final Allele DEL_ALLELE = Allele.create("<DEL>", false);
        final Allele REF_ALLELE = Allele.create("N", true);
        while ((line = r.readLine()) != null) {
            if (StringUtil.isBlank(line))
                continue;
            tokens = tab.split(line);
            if (tokens.length != 3 + samples.size()) {
                throw new JvarkitException.TokenErrors("expected " + (samples.size() + 3) + "columns.", tokens);
            }
            final Set<Allele> alleles = new HashSet<>();
            alleles.add(REF_ALLELE);
            final VariantContextBuilder vcb = new VariantContextBuilder();
            vcb.chr(tokens[0]);
            vcb.start(Integer.parseInt(tokens[1]));
            final int chromEnd = Integer.parseInt(tokens[2]);
            vcb.stop(chromEnd);
            vcb.attribute(VCFConstants.END_KEY, chromEnd);
            if (dict != null) {
                final SAMSequenceRecord ssr = dict.getSequence(tokens[0]);
                if (ssr == null) {
                    LOG.error(JvarkitException.ContigNotFoundInDictionary.getMessage(tokens[0], dict));
                    return -1;
                }
                if (chromEnd > ssr.getSequenceLength()) {
                    LOG.warn("WARNING sequence length in " + line + " is greater than in dictionary ");
                }
            }
            int count_dup = 0;
            int count_del = 0;
            final List<Genotype> genotypes = new ArrayList<>(samples.size());
            for (int i = 3; i < tokens.length; i++) {
                final float f = Float.parseFloat(tokens[i]);
                if (f < 0 || Float.isNaN(f) || !Float.isFinite(f)) {
                    LOG.error("Bad fold " + f + " in " + line);
                }
                final GenotypeBuilder gb;
                if (f <= this.deletionTreshold) {
                    gb = new GenotypeBuilder(samples.get(i - 3), Collections.singletonList(DEL_ALLELE));
                    alleles.add(DEL_ALLELE);
                    gb.attribute(formatIsDeletion.getID(), 1);
                    count_del++;
                } else if (f >= this.duplicationTreshold) {
                    gb = new GenotypeBuilder(samples.get(i - 3), Collections.singletonList(DUP_ALLELE));
                    alleles.add(DUP_ALLELE);
                    gb.attribute(formatIsDuplication.getID(), 1);
                    count_dup++;
                } else {
                    gb = new GenotypeBuilder(samples.get(i - 3), Collections.singletonList(REF_ALLELE));
                    gb.attribute(formatIsDuplication.getID(), 0);
                }
                gb.attribute(foldHeader.getID(), f);
                genotypes.add(gb.make());
            }
            vcb.alleles(alleles);
            vcb.genotypes(genotypes);
            if (count_dup == samples.size() && samples.size() != 1) {
                vcb.filter(filterAllDup.getID());
            }
            if (count_del == samples.size() && samples.size() != 1) {
                vcb.filter(filterAllDel.getID());
            }
            if (count_dup == 0 && count_del == 0) {
                vcb.filter(filterNoSV.getID());
            }
            vcb.attribute(infoNumDel.getID(), count_del);
            vcb.attribute(infoNumDup.getID(), count_dup);
            vcw.add(vcb.make());
        }
        vcw.close();
        vcw = null;
        r.close();
        r = null;
        return 0;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(r);
        CloserUtil.close(vcw);
    }
}

Example 78 with VCFHeader

use of htsjdk.variant.vcf.VCFHeader 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 79 with VCFHeader

use of htsjdk.variant.vcf.VCFHeader in project jvarkit by lindenb.

the class NgsFilesScanner method readVCF.

@Override
protected void readVCF(File f) {
    if (!f.canRead())
        return;
    LOG.debug("readVCF  " + f);
    VcfIterator r = null;
    InputStream in = null;
    try {
        r = VCFUtils.createVcfIteratorFromFile(f);
        VCFHeader header = r.getHeader();
        StringWriter sw = new StringWriter();
        XMLOutputFactory xof = XMLOutputFactory.newFactory();
        XMLStreamWriter out = xof.createXMLStreamWriter(new StreamResult(sw));
        out.writeStartElement("vcf");
        writeFile(out, f);
        out.writeStartElement("samples");
        for (String sample : header.getSampleNamesInOrder()) {
            out.writeStartElement("sample");
            out.writeCharacters(sample);
            out.writeEndElement();
        }
        out.writeEndElement();
        out.writeEndElement();
        out.flush();
        out.close();
        sw.flush();
        put(f, sw.toString());
    } catch (Exception err) {
        LOG.error(err);
    } finally {
        CloserUtil.close(r);
        CloserUtil.close(in);
    }
}

Example 80 with VCFHeader

use of htsjdk.variant.vcf.VCFHeader in project jvarkit by lindenb.

the class NgsFilesSummary method readVCF.

@Override
protected void readVCF(final File f) {
    if (!f.canRead())
        return;
    LOG.debug("readVCF  " + f);
    VcfIterator r = null;
    InputStream in = null;
    try {
        in = IOUtils.openFileForReading(f);
        r = new VcfIteratorImpl(in);
        VCFHeader header = r.getHeader();
        for (final String sample : header.getSampleNamesInOrder()) {
            print(sample, InfoType.VCF, f);
        }
    } catch (final Exception err) {
        LOG.error(err);
    } finally {
        CloserUtil.close(r);
        CloserUtil.close(in);
    }
}