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

Example 96 with VCFIterator

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

the class VcfToBam method doWork.

@Override
public int doWork(final List<String> args) {
    if (this.faidx == null) {
        LOG.error("No REF defined");
        return -1;
    }
    if (readSize <= 0) {
        LOG.error("bad read size");
        return -1;
    }
    if (fragmentSize <= readSize * 2) {
        LOG.error("bad fragment size");
        return -1;
    }
    VCFIterator iter = null;
    try {
        this.indexedFastaSequenceFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(this.faidx);
        iter = super.openVCFIterator(super.oneFileOrNull(args));
        run(iter);
        return 0;
    } catch (final Throwable err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(iter);
    }
}

Example 97 with VCFIterator

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

the class VcfToRdf method scanVCF.

private void scanVCF(final File filein) throws IOException {
    VCFIterator in = null;
    URI source = null;
    try {
        if (filein != null)
            source = filein.toURI();
        in = (filein == null ? VCFUtils.createVCFIteratorStdin() : VCFUtils.createVCFIteratorFromFile(filein));
        final VCFHeader header = in.getHeader();
        final VepPredictionParser vepPredictionParser = new VepPredictionParserFactory(header).get();
        writeHeader(header, source);
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header);
        while (in.hasNext()) {
            if (this.w.checkError()) {
                LOG.warn("I/O interruption");
                break;
            }
            final VariantContext ctx = progress.watch(in.next());
            /* Variant */
            final URI variant = URI.create("urn:variant/" + ctx.getContig() + ":" + ctx.getStart() + ":" + ctx.getReference().getBaseString());
            emit(variant, "rdf:type", "vcf:Variant", "vcf:chrom", URI.create("urn:chrom/" + ctx.getContig()), "vcf:position", ctx.getStart(), "vcf:ref", ctx.getReference().getBaseString(), "vcf:id", (ctx.hasID() ? ctx.getID() : null), "vcf:qual", (ctx.hasLog10PError() ? ctx.getPhredScaledQual() : null));
            if (this.printAlleles) {
                for (final Allele alt : ctx.getAlternateAlleles()) {
                    emit(variant, "vcf:alt", alt.getBaseString());
                }
            }
            if (this.printFilters) {
                for (final String f : ctx.getFilters()) {
                    emit(variant, "vcf:filter", URI.create("urn:filter/" + f));
                }
            }
            if (this.printVep) {
                for (final VepPrediction prediction : vepPredictionParser.getPredictions(ctx)) {
                /* 
					final List<Object> L=new ArrayList<>();
					L.add("rdf:type");L.add("vep:Prediction");
					L.add("vcf:variant"); L.add(variant);
					L.add("vcf:allele");L.add(prediction.getAllele().getBaseString());
					for(final SequenceOntologyTree.Term term:prediction.getSOTerms())
						{
						L.add("vcf:so");
						L.add(URI.create(term.getUri()));
						}
					if(prediction.getEnsemblTranscript()!=null)
						{
						final  URI transcriptid=URI.create("http://www.ensembl.org/id/"+prediction.getEnsemblTranscript());
						L.add("vep:transcript");
						L.add(transcriptid);

						
						if(prediction.getEnsemblGene()!=null)
							{
							emit(transcriptid,
								"uniprot:transcribedFrom",//used  in uniprot dump
								URI.create("http://www.ensembl.org/id/"+prediction.getEnsemblGene())
								);
							}
						
						if(prediction.getEnsemblProtein()!=null)
							{
							emit(
								transcriptid,
								"uniprot:translatedTo",//used  in uniprot dump
								URI.create("http://www.ensembl.org/id/"+prediction.getEnsemblProtein())
								);
							}
						}
					
					
					
					emit(
						URI.create("urn:vep/"+(++id_generator)),
						L.toArray()
						);
					*/
                }
            }
            if (this.printGenotypes) {
                for (final String sample : ctx.getSampleNames()) {
                    final Genotype g = ctx.getGenotype(sample);
                    final List<Object> L = new ArrayList<>();
                    L.add("vcf:sample");
                    L.add(URI.create("urn:sample/" + sample));
                    L.add("vcf:variant");
                    L.add(variant);
                    L.add("rdf:type");
                    L.add("vcf:Genotype");
                    if (g.hasDP()) {
                        L.add("vcf:dp");
                        L.add(g.getDP());
                    }
                    if (g.hasGQ()) {
                        L.add("vcf:gq");
                        L.add(g.getGQ());
                    }
                    if (g.isCalled()) {
                        if (g.isHet()) {
                            if (g.isHetNonRef()) {
                                L.add("rdf:type");
                                L.add("vcf:HetNonRefGenotype");
                            } else {
                                L.add("rdf:type");
                                L.add("vcf:HetGenotype");
                            }
                        } else if (g.isHom()) {
                            if (g.isHomRef()) {
                                L.add("rdf:type");
                                L.add("vcf:HomRefGenotype");
                            } else {
                                L.add("rdf:type");
                                L.add("vcf:HomVarGenotype");
                            }
                        }
                        for (final Allele a : g.getAlleles()) {
                            L.add("vcf:allele");
                            L.add(a.getBaseString());
                        }
                    }
                    emit(URI.create("urn:gt/" + ctx.getContig() + ":" + ctx.getStart() + ":" + ctx.getReference().getBaseString() + ":" + sample), L.toArray());
                }
            }
        }
        in.close();
        in = null;
        progress.finish();
    } catch (final Exception e) {
        throw new IOException(e);
    } finally {
        CloserUtil.close(in);
    }
}

Example 98 with VCFIterator

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

the class VcfToTable method doWork.

@Override
public int doWork(final List<String> args) {
    VCFIterator in = null;
    try {
        in = super.openVCFIterator(oneFileOrNull(args));
        viewer.writeHeader(in.getHeader());
        while (!this.viewer.checkError() && in.hasNext()) {
            viewer.add(in.next());
        }
        viewer.close();
        viewer = null;
        in.close();
        in = null;
        return 0;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(in);
        CloserUtil.close(viewer);
    }
}