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

Example 11 with VCFInfoHeaderLine

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

the class MiniCaller method doWork.

@Override
public int doWork(final List<String> args) {
    ConcatSam.ConcatSamIterator iter = null;
    try {
        if (this.fastaFile == null) {
            LOG.error("no REF");
            return -1;
        }
        /* load faid */
        final ReferenceGenomeFactory referenceGenomeFactory = new ReferenceGenomeFactory();
        this.referenceGenome = referenceGenomeFactory.openFastaFile(this.fastaFile);
        this.dictionary = this.referenceGenome.getDictionary();
        if (this.dictionary == null) {
            LOG.error(JvarkitException.FastaDictionaryMissing.getMessage(this.fastaFile.getPath()));
        }
        /* create sam record iterator */
        iter = new ConcatSam.Factory().addInterval(this.rgnStr).setEnableUnrollList(true).open(args);
        final SAMFileHeader samFileheader = iter.getFileHeader();
        final SAMSequenceDictionary dict = samFileheader.getSequenceDictionary();
        if (dict == null) {
            LOG.error(JvarkitException.BamDictionaryMissing.getMessage(String.join(", ", args)));
            return -1;
        }
        if (!SequenceUtil.areSequenceDictionariesEqual(dict, this.dictionary)) {
            LOG.error(JvarkitException.DictionariesAreNotTheSame.getMessage(dict, this.dictionary));
            return -1;
        }
        final List<SAMReadGroupRecord> groups = samFileheader.getReadGroups();
        if (groups == null || groups.isEmpty()) {
            LOG.error("No group defined in input");
            return -1;
        }
        final Set<String> sampleSet = groups.stream().map(srgr -> this.samRecordPartition.apply(srgr, samRecordPartition.name())).collect(Collectors.toSet());
        /* create VCF metadata */
        final Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
        metaData.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_KEY));
        metaData.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.DEPTH_KEY));
        metaData.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.DEPTH_KEY));
        metaData.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY));
        metaData.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY));
        metaData.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY));
        metaData.add(new VCFFormatHeaderLine("DPG", // one value of each genotype
        VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Depth for each allele"));
        metaData.add(new VCFFormatHeaderLine("DP4", 4, VCFHeaderLineType.Integer, "Depth ReforAlt|Strand : RF,RR,AF,AR"));
        metaData.add(new VCFInfoHeaderLine("INDEL", 1, VCFHeaderLineType.Flag, "Variant is indel"));
        // addMetaData(metaData);
        final VCFHeader vcfHeader = new VCFHeader(metaData, sampleSet);
        vcfHeader.setSequenceDictionary(this.dictionary);
        /* create variant context */
        this.variantContextWriter = super.openVariantContextWriter(outputFile);
        this.variantContextWriter.writeHeader(vcfHeader);
        ReferenceContig genomicSeq = null;
        SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(this.dictionary);
        for (; ; ) {
            SAMRecord rec = null;
            if (iter.hasNext()) {
                rec = progress.watch(iter.next());
                if (rec.getReadUnmappedFlag())
                    continue;
                if (this.readFilter.filterOut(rec))
                    continue;
                /* flush buffer if needed */
                while (!this.buffer.isEmpty() && (this.buffer.get(0).tid < rec.getReferenceIndex() || (this.buffer.get(0).tid == rec.getReferenceIndex() && (this.buffer.get(0).getEnd()) < rec.getAlignmentStart()))) {
                    this.buffer.remove(0).print();
                }
                /* get genomic sequence at this position */
                if (genomicSeq == null || !genomicSeq.getContig().equals(rec.getContig())) {
                    genomicSeq = this.referenceGenome.getContig(rec.getContig());
                }
                final Cigar cigar = rec.getCigar();
                if (cigar == null)
                    continue;
                int readPos = 0;
                // 0 based-reference
                int refPos0 = rec.getAlignmentStart() - 1;
                final byte[] bases = rec.getReadBases();
                final byte[] quals = rec.getBaseQualities();
                final String sampleName = this.samRecordPartition.getPartion(rec, samRecordPartition.name());
                for (final CigarElement ce : cigar.getCigarElements()) {
                    final CigarOperator op = ce.getOperator();
                    switch(op) {
                        case P:
                            break;
                        case H:
                            break;
                        case S:
                            readPos += ce.getLength();
                            break;
                        // go
                        case N:
                        case D:
                            {
                                if (// we need base before deletion
                                refPos0 > 0) {
                                    char refBase = genomicSeq.charAt(refPos0 - 1);
                                    /* we use base before deletion */
                                    final StringBuilder sb = new StringBuilder(ce.getLength());
                                    sb.append(refBase);
                                    for (int i = 0; i < ce.getLength(); ++i) {
                                        sb.append(genomicSeq.charAt(refPos0 + i));
                                    }
                                    findContext(rec.getReferenceIndex(), // we use base *before deletion */
                                    refPos0 - 1, Allele.create(sb.toString(), true)).getSample(sampleName).getAllele(Allele.create(String.valueOf(refBase), false)).incr(rec.getReadNegativeStrandFlag());
                                }
                                refPos0 += ce.getLength();
                                break;
                            }
                        case I:
                            {
                                if (refPos0 > 0) {
                                    // float qual=0;
                                    char refBase = Character.toUpperCase(genomicSeq.charAt(refPos0 - 1));
                                    final StringBuilder sb = new StringBuilder(1 + ce.getLength());
                                    sb.append(refBase);
                                    for (int i = 0; i < ce.getLength(); ++i) {
                                        sb.append((char) bases[readPos + i]);
                                    // qual+=(readPos + i < quals.length?quals[ readPos + i]:0);
                                    }
                                    findContext(rec.getReferenceIndex(), // we use base *before deletion */
                                    refPos0 - 1, Allele.create(String.valueOf(refBase), true)).getSample(sampleName).getAllele(Allele.create(sb.toString().toUpperCase(), false)).incr(rec.getReadNegativeStrandFlag());
                                }
                                readPos += ce.getLength();
                                break;
                            }
                        case EQ:
                        case M:
                        case X:
                            {
                                for (int i = 0; i < ce.getLength(); ++i) {
                                    findContext(rec.getReferenceIndex(), refPos0 + i, Allele.create(String.valueOf(genomicSeq.charAt(refPos0 + i)), true)).getSample(sampleName).getAllele(Allele.create(String.valueOf((char) bases[readPos + i]), false)).incr(rec.getReadNegativeStrandFlag());
                                }
                                readPos += ce.getLength();
                                refPos0 += ce.getLength();
                                break;
                            }
                        default:
                            throw new IllegalStateException("Case statement didn't deal with cigar op: " + op);
                    }
                }
            } else {
                break;
            }
        }
        while (!buffer.isEmpty()) buffer.remove(0).print();
        progress.finish();
        iter.close();
        iter = null;
        this.variantContextWriter.close();
        this.variantContextWriter = null;
        return RETURN_OK;
    } catch (Exception e) {
        LOG.error(e);
        return -1;
    } finally {
        CloserUtil.close(iter);
        CloserUtil.close(this.referenceGenome);
        CloserUtil.close(this.variantContextWriter);
    }
}

Example 12 with VCFInfoHeaderLine

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

the class EvsToVcf method doWork.

@Override
public int doWork(List<String> args) {
    VariantContextWriter out = null;
    try {
        if (!args.isEmpty()) {
            LOG.error("Illegal number of arguments");
            return -1;
        }
        JAXBContext jc = JAXBContext.newInstance(SnpData.class);
        Unmarshaller unmarshaller = jc.createUnmarshaller();
        out = VCFUtils.createVariantContextWriterToStdout();
        SAMSequenceDictionary dict = new SAMSequenceDictionary();
        _fillDict(dict, "1", 249250621);
        _fillDict(dict, "2", 243199373);
        _fillDict(dict, "3", 198022430);
        _fillDict(dict, "4", 191154276);
        _fillDict(dict, "5", 180915260);
        _fillDict(dict, "6", 171115067);
        _fillDict(dict, "7", 159138663);
        _fillDict(dict, "8", 146364022);
        _fillDict(dict, "9", 141213431);
        _fillDict(dict, "10", 135534747);
        _fillDict(dict, "11", 135006516);
        _fillDict(dict, "12", 133851895);
        _fillDict(dict, "13", 115169878);
        _fillDict(dict, "14", 107349540);
        _fillDict(dict, "15", 102531392);
        _fillDict(dict, "16", 90354753);
        _fillDict(dict, "17", 81195210);
        _fillDict(dict, "18", 78077248);
        _fillDict(dict, "19", 59128983);
        _fillDict(dict, "20", 63025520);
        _fillDict(dict, "21", 48129895);
        _fillDict(dict, "22", 51304566);
        _fillDict(dict, "X", 155270560);
        _fillDict(dict, "Y", 59373566);
        _fillDict(dict, "MT", 16569);
        VCFHeader header = new VCFHeader();
        header.setSequenceDictionary(dict);
        header.addMetaDataLine(new VCFInfoHeaderLine("CONS", VCFHeaderLineCount.INTEGER, VCFHeaderLineType.Float, "conservationScore"));
        header.addMetaDataLine(new VCFInfoHeaderLine("GERP", VCFHeaderLineCount.INTEGER, VCFHeaderLineType.Float, "conservationScoreGERP"));
        header.addMetaDataLine(new VCFInfoHeaderLine("uaMAF", VCFHeaderLineCount.INTEGER, VCFHeaderLineType.Float, "conservationScoreGERP"));
        header.addMetaDataLine(new VCFInfoHeaderLine("aaMAF", VCFHeaderLineCount.INTEGER, VCFHeaderLineType.Float, "conservationScoreGERP"));
        header.addMetaDataLine(new VCFInfoHeaderLine("totalMAF", VCFHeaderLineCount.INTEGER, VCFHeaderLineType.Float, "conservationScoreGERP"));
        header.addMetaDataLine(new VCFInfoHeaderLine("DP", VCFHeaderLineCount.INTEGER, VCFHeaderLineType.Integer, "conservationScoreGERP"));
        header.addMetaDataLine(new VCFHeaderLine(getClass().getSimpleName() + "CmdLine", String.valueOf(getProgramCommandLine())));
        header.addMetaDataLine(new VCFHeaderLine(getClass().getSimpleName() + "Version", String.valueOf(getVersion())));
        header.addMetaDataLine(new VCFHeaderLine(getClass().getSimpleName() + "HtsJdkVersion", HtsjdkVersion.getVersion()));
        header.addMetaDataLine(new VCFHeaderLine(getClass().getSimpleName() + "HtsJdkHome", HtsjdkVersion.getHome()));
        out.writeHeader(header);
        Pattern comma = Pattern.compile("[,]");
        XMLInputFactory xif = XMLInputFactory.newFactory();
        xif.setProperty(XMLInputFactory.IS_NAMESPACE_AWARE, false);
        XMLEventReader xmlr = xif.createXMLEventReader(System.in);
        while (xmlr.hasNext() && !System.out.checkError()) {
            XMLEvent evt = xmlr.peek();
            if (!evt.isStartElement() || !evt.asStartElement().getName().getLocalPart().equals("snpList")) {
                xmlr.nextEvent();
                continue;
            }
            SnpData snpData = unmarshaller.unmarshal(xmlr, SnpData.class).getValue();
            VariantContextBuilder vcb = new VariantContextBuilder();
            Set<Allele> alleles = new HashSet<Allele>();
            alleles.add(Allele.create(snpData.getRefAllele(), true));
            for (String s : comma.split(snpData.getAltAlleles())) {
                if (isEmpty(s))
                    continue;
                alleles.add(Allele.create(s, false));
            }
            vcb.chr(snpData.getChromosome());
            vcb.start(snpData.getChrPosition());
            vcb.stop(snpData.getChrPosition() + snpData.getRefAllele().length() - 1);
            if (!isEmpty(snpData.getRsIds()) && !snpData.getRsIds().equals("none")) {
                vcb.id(snpData.getRsIds());
            }
            vcb.alleles(alleles);
            Float d = parseDouble(snpData.getConservationScore());
            if (d != null) {
                vcb.attribute("CONS", d);
            }
            d = parseDouble(snpData.getConservationScoreGERP());
            if (d != null) {
                vcb.attribute("GERP", d);
            }
            vcb.attribute("uaMAF", (float) snpData.getUaMAF());
            vcb.attribute("aaMAF", (float) snpData.getAaMAF());
            vcb.attribute("totalMAF", (float) snpData.getTotalMAF());
            vcb.attribute("DP", snpData.getAvgSampleReadDepth());
            out.add(vcb.make());
        }
        xmlr.close();
        out.close();
        return 0;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(out);
    }
}

Example 13 with VCFInfoHeaderLine

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

the class VcfStage method buildInfoHeaderTab.

/**
 * build a table describing the INFO column
 */
private Tab buildInfoHeaderTab(final VCFHeader header) {
    final TableView<VCFInfoHeaderLine> table = new TableView<>(FXCollections.observableArrayList(header.getInfoHeaderLines()));
    table.getColumns().add(makeColumn("ID", F -> F.getID()));
    table.getColumns().add(makeColumn("Type", F -> F.getType() == null ? null : F.getType().name()));
    table.getColumns().add(makeColumn("Count", F -> F.isFixedCount() ? F.getCount() : null));
    table.getColumns().add(makeColumn("Description", F -> F.getDescription()));
    final Tab tab = new Tab("INFO", table);
    tab.setClosable(false);
    table.setPlaceholder(new Label("No INFO defined."));
    return tab;
}

Example 14 with VCFInfoHeaderLine

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

the class VCFPredictions method doVcfToVcf.

@Override
protected int doVcfToVcf(final String inputName, final VcfIterator r, VariantContextWriter w) {
    ReferenceContig genomicSequence = null;
    try {
        LOG.info("opening REF:" + this.referenceGenomeSource);
        this.referenceGenome = new ReferenceGenomeFactory().open(this.referenceGenomeSource);
        loadKnownGenesFromUri();
        final VCFHeader header = (VCFHeader) r.getHeader();
        final ContigNameConverter contigNameConverter = ContigNameConverter.fromOneDictionary(this.referenceGenome.getDictionary());
        contigNameConverter.setOnNotFound(OnNotFound.SKIP);
        final VCFHeader h2 = new VCFHeader(header);
        addMetaData(h2);
        switch(this.outputSyntax) {
            case Vep:
                {
                    h2.addMetaDataLine(new VCFInfoHeaderLine("CSQ", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Consequence type as predicted by VEP" + ". Format: Allele|Feature|Feature_type|Consequence|CDS_position|Protein_position|Amino_acids|Codons"));
                    break;
                }
            case SnpEff:
                {
                    h2.addMetaDataLine(new VCFInfoHeaderLine("ANN", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'"));
                    break;
                }
            default:
                {
                    final StringBuilder format = new StringBuilder();
                    for (FORMAT1 f : FORMAT1.values()) {
                        if (format.length() > 0)
                            format.append("|");
                        format.append(f.name());
                    }
                    h2.addMetaDataLine(new VCFInfoHeaderLine(TAG, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Prediction from " + getClass().getSimpleName() + ". Format: " + format));
                    break;
                }
        }
        w.writeHeader(h2);
        final SequenceOntologyTree soTree = SequenceOntologyTree.getInstance();
        final SequenceOntologyTree.Term so_intron = soTree.getTermByAcn("SO:0001627");
        final SequenceOntologyTree.Term so_exon = soTree.getTermByAcn("SO:0001791");
        final SequenceOntologyTree.Term so_splice_donor = soTree.getTermByAcn("SO:0001575");
        final SequenceOntologyTree.Term so_splice_acceptor = soTree.getTermByAcn("SO:0001574");
        final SequenceOntologyTree.Term so_5_prime_UTR_variant = soTree.getTermByAcn("SO:0001623");
        final SequenceOntologyTree.Term so_3_prime_UTR_variant = soTree.getTermByAcn("SO:0001624");
        final SequenceOntologyTree.Term so_splicing_variant = soTree.getTermByAcn("SO:0001568");
        final SequenceOntologyTree.Term so_stop_lost = soTree.getTermByAcn("SO:0001578");
        final SequenceOntologyTree.Term so_stop_gained = soTree.getTermByAcn("SO:0001587");
        final SequenceOntologyTree.Term so_coding_synonymous = soTree.getTermByAcn("SO:0001819");
        final SequenceOntologyTree.Term so_coding_non_synonymous = soTree.getTermByAcn("SO:0001583");
        final SequenceOntologyTree.Term so_intergenic = soTree.getTermByAcn("SO:0001628");
        final SequenceOntologyTree.Term so_nc_transcript_variant = soTree.getTermByAcn("SO:0001619");
        final SequenceOntologyTree.Term so_non_coding_exon_variant = soTree.getTermByAcn("SO:0001792");
        final SequenceOntologyTree.Term _2KB_upstream_variant = soTree.getTermByAcn("SO:0001636");
        final SequenceOntologyTree.Term _5KB_upstream_variant = soTree.getTermByAcn("SO:0001635");
        final SequenceOntologyTree.Term _5KB_downstream_variant = soTree.getTermByAcn("SO:0001633");
        final SequenceOntologyTree.Term _500bp_downstream_variant = soTree.getTermByAcn("SO:0001634");
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header);
        while (r.hasNext()) {
            final VariantContext ctx = progress.watch(r.next());
            final String normalizedContig = contigNameConverter.apply(ctx.getContig());
            final List<KnownGene> genes = new ArrayList<>();
            if (!StringUtil.isBlank(normalizedContig)) {
                for (final List<KnownGene> l2 : this.knownGenes.getOverlapping(new Interval(normalizedContig, ctx.getStart(), // 1-based
                ctx.getEnd()))) {
                    genes.addAll(l2);
                }
            }
            final List<Annotation> ctx_annotations = new ArrayList<Annotation>();
            if (genes == null || genes.isEmpty()) {
                // intergenic
                Annotation a = new Annotation();
                a.seqont.add(so_intergenic);
                ctx_annotations.add(a);
            } else {
                if (genomicSequence == null || !genomicSequence.hasName(normalizedContig)) {
                    LOG.info("getting genomic Sequence for " + normalizedContig);
                    genomicSequence = this.referenceGenome.getContig(normalizedContig);
                    if (genomicSequence == null)
                        throw new JvarkitException.ContigNotFoundInDictionary(normalizedContig, this.referenceGenome.getDictionary());
                }
                for (final KnownGene gene : genes) {
                    final GeneticCode geneticCode = GeneticCode.getStandard();
                    for (final Allele alt2 : ctx.getAlternateAlleles()) {
                        if (alt2.isNoCall())
                            continue;
                        if (alt2.isSymbolic()) {
                            LOG.warn("symbolic allele are not handled... " + alt2.getDisplayString());
                            continue;
                        }
                        if (alt2.isReference())
                            continue;
                        final Annotation annotations = new Annotation();
                        annotations.kg = gene;
                        annotations.alt2 = alt2;
                        if (gene.isNonCoding()) {
                            annotations.seqont.add(so_nc_transcript_variant);
                            continue;
                        }
                        ctx_annotations.add(annotations);
                        StringBuilder wildRNA = null;
                        ProteinCharSequence wildProt = null;
                        ProteinCharSequence mutProt = null;
                        MutedSequence mutRNA = null;
                        int position_in_cds = -1;
                        final int position = ctx.getStart() - 1;
                        if (!String.valueOf(genomicSequence.charAt(position)).equalsIgnoreCase(ctx.getReference().getBaseString())) {
                            if (isSimpleBase(ctx.getReference())) {
                                LOG.warn("Warning REF!=GENOMIC SEQ!!! at " + position + "/" + ctx.getReference());
                            }
                            continue;
                        }
                        if (gene.isPositiveStrand()) {
                            if (position < gene.getTxStart() - 2000) {
                                annotations.seqont.add(_5KB_upstream_variant);
                            } else if (position < gene.getTxStart()) {
                                annotations.seqont.add(_2KB_upstream_variant);
                            } else if (position >= gene.getTxEnd() + 500) {
                                annotations.seqont.add(_5KB_downstream_variant);
                            } else if (position >= gene.getTxEnd()) {
                                annotations.seqont.add(_500bp_downstream_variant);
                            } else if (position < gene.getCdsStart()) {
                                // UTR5
                                annotations.seqont.add(so_5_prime_UTR_variant);
                            } else if (gene.getCdsEnd() <= position) {
                                annotations.seqont.add(so_3_prime_UTR_variant);
                            } else {
                                int exon_index = 0;
                                while (exon_index < gene.getExonCount()) {
                                    final KnownGene.Exon exon = gene.getExon(exon_index);
                                    for (int i = exon.getStart(); i < exon.getEnd(); ++i) {
                                        if (i == position) {
                                            annotations.exon_name = exon.getName();
                                            if (exon.isNonCoding()) {
                                                annotations.seqont.add(so_non_coding_exon_variant);
                                            }
                                        }
                                        if (i < gene.getTxStart())
                                            continue;
                                        if (i < gene.getCdsStart())
                                            continue;
                                        if (i >= gene.getCdsEnd())
                                            break;
                                        if (wildRNA == null) {
                                            wildRNA = new StringBuilder();
                                            mutRNA = new MutedSequence(wildRNA);
                                        }
                                        if (i == position) {
                                            annotations.seqont.add(so_exon);
                                            annotations.exon_name = exon.getName();
                                            position_in_cds = wildRNA.length();
                                            annotations.position_cds = position_in_cds;
                                            // in splicing ?
                                            if (exon.isSplicing(position)) {
                                                if (exon.isSplicingAcceptor(position)) {
                                                    // SPLICING_ACCEPTOR
                                                    annotations.seqont.add(so_splice_acceptor);
                                                } else if (exon.isSplicingDonor(position)) {
                                                    // SPLICING_DONOR
                                                    annotations.seqont.add(so_splice_donor);
                                                } else // ??
                                                {
                                                    annotations.seqont.add(so_splicing_variant);
                                                }
                                            }
                                        }
                                        wildRNA.append(genomicSequence.charAt(i));
                                        if (i == position && isSimpleBase(alt2) && isSimpleBase(ctx.getReference())) {
                                            mutRNA.put(position_in_cds, alt2.getBaseString().charAt(0));
                                        }
                                        if (wildRNA.length() % 3 == 0 && wildRNA.length() > 0 && wildProt == null) {
                                            wildProt = new ProteinCharSequence(geneticCode, wildRNA);
                                            mutProt = new ProteinCharSequence(geneticCode, mutRNA);
                                        }
                                    }
                                    final KnownGene.Intron intron = exon.getNextIntron();
                                    if (intron != null && intron.contains(position)) {
                                        annotations.intron_name = intron.getName();
                                        annotations.seqont.add(so_intron);
                                        if (intron.isSplicing(position)) {
                                            if (intron.isSplicingAcceptor(position)) {
                                                annotations.seqont.add(so_splice_acceptor);
                                            } else if (intron.isSplicingDonor(position)) {
                                                annotations.seqont.add(so_splice_donor);
                                            } else // ???
                                            {
                                                annotations.seqont.add(so_splicing_variant);
                                            }
                                        }
                                    }
                                    ++exon_index;
                                }
                            }
                        } else // reverse orientation
                        {
                            if (position >= gene.getTxEnd() + 2000) {
                                annotations.seqont.add(_5KB_upstream_variant);
                            } else if (position >= gene.getTxEnd()) {
                                annotations.seqont.add(_2KB_upstream_variant);
                            } else if (position < gene.getTxStart() - 500) {
                                annotations.seqont.add(_5KB_downstream_variant);
                            } else if (position < gene.getTxStart()) {
                                annotations.seqont.add(_500bp_downstream_variant);
                            } else if (position < gene.getCdsStart()) {
                                annotations.seqont.add(so_3_prime_UTR_variant);
                            } else if (gene.getCdsEnd() <= position) {
                                annotations.seqont.add(so_5_prime_UTR_variant);
                            } else {
                                int exon_index = gene.getExonCount() - 1;
                                while (exon_index >= 0) {
                                    final KnownGene.Exon exon = gene.getExon(exon_index);
                                    for (int i = exon.getEnd() - 1; i >= exon.getStart(); --i) {
                                        if (i == position) {
                                            annotations.exon_name = exon.getName();
                                            if (exon.isNonCoding()) {
                                                annotations.seqont.add(so_non_coding_exon_variant);
                                            }
                                        }
                                        if (i >= gene.getCdsEnd())
                                            continue;
                                        if (i < gene.getCdsStart())
                                            break;
                                        if (wildRNA == null) {
                                            wildRNA = new StringBuilder();
                                            mutRNA = new MutedSequence(wildRNA);
                                        }
                                        if (i == position) {
                                            annotations.seqont.add(so_exon);
                                            position_in_cds = wildRNA.length();
                                            annotations.position_cds = position_in_cds;
                                            // in splicing ?
                                            if (exon.isSplicing(position)) {
                                                if (exon.isSplicingAcceptor(position)) {
                                                    annotations.seqont.add(so_splice_acceptor);
                                                } else if (exon.isSplicingDonor(position)) {
                                                    annotations.seqont.add(so_splice_donor);
                                                } else // ?
                                                {
                                                    annotations.seqont.add(so_splicing_variant);
                                                }
                                            }
                                            if (isSimpleBase(alt2) && isSimpleBase(ctx.getReference())) {
                                                mutRNA.put(position_in_cds, AcidNucleics.complement(alt2.getBaseString().charAt(0)));
                                            }
                                        }
                                        wildRNA.append(AcidNucleics.complement(genomicSequence.charAt(i)));
                                        if (wildRNA.length() % 3 == 0 && wildRNA.length() > 0 && wildProt == null) {
                                            wildProt = new ProteinCharSequence(geneticCode, wildRNA);
                                            mutProt = new ProteinCharSequence(geneticCode, mutRNA);
                                        }
                                    }
                                    final KnownGene.Intron intron = exon.getPrevIntron();
                                    if (intron != null && intron.contains(position)) {
                                        annotations.intron_name = intron.getName();
                                        annotations.seqont.add(so_intron);
                                        if (intron.isSplicing(position)) {
                                            if (intron.isSplicingAcceptor(position)) {
                                                annotations.seqont.add(so_splice_acceptor);
                                            } else if (intron.isSplicingDonor(position)) {
                                                annotations.seqont.add(so_splice_donor);
                                            } else // ?
                                            {
                                                annotations.seqont.add(so_splicing_variant);
                                            }
                                        }
                                    }
                                    --exon_index;
                                }
                            }
                        }
                        if (isSimpleBase(alt2) && isSimpleBase(ctx.getReference()) && wildProt != null && mutProt != null && position_in_cds >= 0) {
                            final int pos_aa = position_in_cds / 3;
                            final int mod = position_in_cds % 3;
                            annotations.wildCodon = ("" + wildRNA.charAt(position_in_cds - mod + 0) + wildRNA.charAt(position_in_cds - mod + 1) + wildRNA.charAt(position_in_cds - mod + 2));
                            annotations.mutCodon = ("" + mutRNA.charAt(position_in_cds - mod + 0) + mutRNA.charAt(position_in_cds - mod + 1) + mutRNA.charAt(position_in_cds - mod + 2));
                            annotations.position_protein = (pos_aa + 1);
                            annotations.wildAA = String.valueOf(wildProt.charAt(pos_aa));
                            annotations.mutAA = (String.valueOf(mutProt.charAt(pos_aa)));
                            annotations.seqont.remove(so_exon);
                            if (isStop(wildProt.charAt(pos_aa)) && !isStop(mutProt.charAt(pos_aa))) {
                                annotations.seqont.add(so_stop_lost);
                            } else if (!isStop(wildProt.charAt(pos_aa)) && isStop(mutProt.charAt(pos_aa))) {
                                annotations.seqont.add(so_stop_gained);
                            } else if (wildProt.charAt(pos_aa) == mutProt.charAt(pos_aa)) {
                                annotations.seqont.add(so_coding_synonymous);
                            } else {
                                annotations.seqont.add(so_coding_non_synonymous);
                            }
                        }
                    }
                }
            }
            final Set<String> info = new HashSet<String>(ctx_annotations.size());
            for (final Annotation a : ctx_annotations) {
                info.add(a.toString());
            }
            final VariantContextBuilder vb = new VariantContextBuilder(ctx);
            final String thetag;
            switch(this.outputSyntax) {
                case Vep:
                    thetag = "CSQ";
                    break;
                case SnpEff:
                    thetag = "ANN";
                    break;
                default:
                    thetag = TAG;
                    break;
            }
            vb.attribute(thetag, info.toArray());
            w.add(vb.make());
        }
        return RETURN_OK;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(this.referenceGenome);
    }
}

Example 15 with VCFInfoHeaderLine

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

the class VcfUcsc method doVcfToVcf.

@Override
protected int doVcfToVcf(final String inputName, final VcfIterator in, final VariantContextWriter out) {
    final String TAG;
    if (StringUtil.isBlank(this.infoTag)) {
        TAG = "UCSC_" + database.toUpperCase() + "_" + table.toUpperCase();
    } else {
        TAG = this.infoTag;
    }
    VCFHeader header = in.getHeader();
    final VCFHeader h2 = new VCFHeader(header);
    h2.addMetaDataLine(new VCFInfoHeaderLine(TAG, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, database + "." + table));
    if (!StringUtil.isBlank(this.filterIn)) {
        h2.addMetaDataLine(new VCFFilterHeaderLine(this.filterIn, "Set by " + this.getClass().getName()));
    } else if (!StringUtil.isBlank(this.filterOut)) {
        h2.addMetaDataLine(new VCFFilterHeaderLine(this.filterOut, "Set by " + this.getClass().getName()));
    }
    h2.addMetaDataLine(new VCFHeaderLine(getClass().getSimpleName() + "CmdLine", String.valueOf(getProgramCommandLine())));
    h2.addMetaDataLine(new VCFHeaderLine(getClass().getSimpleName() + "Version", String.valueOf(getVersion())));
    out.writeHeader(h2);
    final Map<Integer, PreparedStatement> bin2pstmt = new HashMap<>();
    try {
        if (!this.has_bin_column) {
            bin2pstmt.put(0, createPreparedStatement(0));
        }
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header).logger(LOG);
        while (in.hasNext()) {
            final VariantContext ctx = progress.watch(in.next());
            int start0, end0;
            if (// mutation starts *after* the base
            ctx.isIndel()) {
                start0 = ctx.getStart();
                end0 = ctx.getEnd();
            } else {
                start0 = ctx.getStart() - 1;
                end0 = ctx.getEnd();
            }
            // extends left/right
            start0 = Math.max(0, start0 - this.extend_bases);
            end0 += this.extend_bases;
            final Set<String> atts = new HashSet<String>();
            if (this.has_bin_column) {
                final List<Integer> binList = reg2bins(start0, end0);
                PreparedStatement pstmt = bin2pstmt.get(binList.size());
                if (pstmt == null) {
                    LOG.debug("create prepared statemement for bin.size=" + binList.size() + "[" + start0 + ":" + end0 + "]");
                    pstmt = createPreparedStatement(binList.size());
                    bin2pstmt.put(binList.size(), pstmt);
                }
                initPstmt(pstmt, ctx.getContig(), start0, end0);
                for (int x = 0; x < binList.size(); ++x) {
                    pstmt.setInt(4 + x, binList.get(x));
                }
                select(atts, pstmt);
            } else {
                // already defined
                final PreparedStatement pstmt = bin2pstmt.get(0);
                initPstmt(pstmt, ctx.getContig(), start0, end0);
                select(atts, pstmt);
            }
            if (atts.isEmpty() && StringUtil.isBlank(this.filterIn) && StringUtil.isBlank(this.filterOut)) {
                out.add(ctx);
                continue;
            }
            final VariantContextBuilder vcb = new VariantContextBuilder(ctx);
            if (!StringUtil.isBlank(this.filterIn) && !atts.isEmpty()) {
                vcb.filter(this.filterIn);
            } else if (!StringUtil.isBlank(this.filterOut) && atts.isEmpty()) {
                vcb.filter(this.filterOut);
            }
            if (!atts.isEmpty()) {
                vcb.attribute(TAG, atts.toArray());
            }
            out.add(vcb.make());
        }
        progress.finish();
        return 0;
    } catch (final SQLException err) {
        LOG.error(err);
        throw new RuntimeException("SQLError", err);
    } finally {
        for (final PreparedStatement pstmt : bin2pstmt.values()) {
            CloserUtil.close(pstmt);
        }
        bin2pstmt.clear();
    }
}