Examples with VariantContextWriter htsjdk.variant.variantcontext.writer.VariantContextWriter used on opensource projects

Example 61 with VariantContextWriter

use of htsjdk.variant.variantcontext.writer.VariantContextWriter in project jvarkit by lindenb.

the class VcfTail method doVcfToVcf.

@Override
protected int doVcfToVcf(final String inputName, final VcfIterator in, final VariantContextWriter delegate) {
    try {
        final VariantContextWriter out = this.component.open(delegate);
        out.writeHeader(in.getHeader());
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(in.getHeader()).logger(LOG);
        while (in.hasNext()) {
            out.add(progress.watch(in.next()));
        }
        progress.finish();
        out.close();
        return 0;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    }
}

Example 62 with VariantContextWriter

use of htsjdk.variant.variantcontext.writer.VariantContextWriter in project jvarkit by lindenb.

the class VcfOptimizePedForSkat method exec.

private void exec(final long generation, final VCFHeader header, final List<VariantContext> variants, final List<Pedigree.Person> samples, final SkatFactory.SkatExecutor skatExecutor) {
    final Solution solution = new Solution();
    solution.generation = generation;
    String origin = "random";
    if (generation != 0) {
        int nRemove = 1 + this.random.nextInt(this.nSamplesRemove);
        if (generation == 1 && this.bootstrapSamples != null) {
            origin = "bootstrap";
            for (final String sample : this.bootstrapSamples.split("[; ,]")) {
                if (StringUtil.isBlank(sample))
                    continue;
                if (!samples.stream().anyMatch(S -> S.getId().equals(sample))) {
                    throw new JvarkitException.UserError("Sample " + sample + " not found in effective pedigree.");
                }
                LOG.info("bootstraping with " + sample);
                solution.sampleSet.add(sample);
            }
        } else if (generation % 5 == 0 && !this.bestSolutions.isEmpty()) {
            int sol_index = this.random.nextInt(Math.min(this.max_results_output, this.bestSolutions.size()));
            final List<String> list = new ArrayList<>(this.bestSolutions.get(sol_index).sampleSet);
            if (list.size() > 1 && this.random.nextBoolean()) {
                origin = "best-minus-random";
                list.remove(this.random.nextInt(list.size()));
            } else if (list.size() < nRemove) {
                origin = "best-plus-random";
                list.add(samples.get(this.random.nextInt(samples.size())).getId());
            }
            solution.sampleSet.addAll(list);
        } else if (generation % 7 == 0 && this.bestSolutions.size() > 2) {
            final Set<String> set = new HashSet<>(this.bestSolutions.get(0).sampleSet);
            set.addAll(this.bestSolutions.get(1).sampleSet);
            final List<String> bestsamples = new ArrayList<>(set);
            Collections.shuffle(bestsamples, this.random);
            while (bestsamples.size() > nRemove) {
                bestsamples.remove(0);
            }
            solution.sampleSet.addAll(bestsamples);
            origin = "best0-plus-best1";
        } else {
            while (nRemove > 0) {
                final String sampleId;
                if (generation % 3 == 0L && nRemove % 2 == 0 && this.bestSolutions.size() > 0 && !this.bestSolutions.get(0).sampleSet.isEmpty()) {
                    final List<String> bestsamples = new ArrayList<>(this.bestSolutions.get(0).sampleSet);
                    sampleId = bestsamples.get(this.random.nextInt(bestsamples.size()));
                    origin = "random-plus-best0";
                } else {
                    sampleId = samples.get(this.random.nextInt(samples.size())).getId();
                }
                solution.sampleSet.add(sampleId);
                nRemove--;
            }
        }
    } else {
        origin = "original";
    }
    if (generation > 0 && solution.sampleSet.isEmpty())
        return;
    while (solution.sampleSet.size() > this.nSamplesRemove) {
        LOG.warn("Hum... to many for " + origin);
        final List<String> L = new ArrayList<>(solution.sampleSet);
        while (L.size() > 0 && L.size() > this.nSamplesRemove) L.remove(this.random.nextInt(L.size()));
        solution.sampleSet.clear();
        solution.sampleSet.addAll(L);
    }
    if (this.bestSolutions.contains(solution))
        return;
    solution.origin = origin;
    final List<Pedigree.Person> ped2 = new ArrayList<>(samples);
    ped2.removeIf(I -> solution.sampleSet.contains(I.getId()));
    if (ped2.isEmpty())
        return;
    if (!ped2.stream().anyMatch(P -> P.isAffected()))
        return;
    if (!ped2.stream().anyMatch(P -> P.isUnaffected()))
        return;
    // test MAF et Fisher
    final VCFHeader header2 = new VCFHeader(header.getMetaDataInInputOrder(), header.getSampleNamesInOrder());
    final VcfBurdenFisherH.CtxWriterFactory fisherhFactory = new VcfBurdenFisherH.CtxWriterFactory();
    fisherhFactory.setCaseControlExtractor((H) -> new HashSet<>(ped2));
    fisherhFactory.setIgnoreFiltered(true);
    final VcfBurdenMAF.CtxWriterFactory mafFactory = new VcfBurdenMAF.CtxWriterFactory();
    mafFactory.setCaseControlExtractor((H) -> new HashSet<>(ped2));
    mafFactory.setIgnoreFiltered(true);
    final VariantCollector collector = new VariantCollector();
    VariantContextWriter vcw = mafFactory.open(collector);
    vcw = fisherhFactory.open(vcw);
    vcw.writeHeader(header2);
    for (final VariantContext vc : variants) {
        vcw.add(vc);
    }
    vcw.close();
    CloserUtil.close(fisherhFactory);
    CloserUtil.close(mafFactory);
    // 
    solution.result = skatExecutor.execute(collector.variants, ped2);
    if (solution.result.isError())
        return;
    if (this.bestSolutions.isEmpty() || solution.compareTo(this.bestSolutions.get(this.bestSolutions.size() - 1)) < 0) {
        this.bestSolutions.add(solution);
        if (this.firstScore == null) {
            this.firstScore = solution.result.getPValue();
        }
        Collections.sort(this.bestSolutions);
        final int BUFFER_RESULT = 1000;
        while (this.bestSolutions.size() > BUFFER_RESULT) {
            this.bestSolutions.remove(this.bestSolutions.size() - 1);
        }
        if (this.bestSolutions.indexOf(solution) < this.max_results_output) {
            final StringBuilder sb = new StringBuilder();
            sb.append(">>> ").append(generation).append("\n");
            this.bestSolutions.stream().limit(this.max_results_output).forEach(S -> sb.append(S).append("\n"));
            sb.append("<<< ").append(generation).append("\n");
            if (outputFile == null) {
                stdout().println(sb.toString());
            } else {
                stderr().println(sb.toString());
                IOUtils.cat(sb.toString(), this.outputFile, false);
            }
        }
    }
}

Example 63 with VariantContextWriter

use of htsjdk.variant.variantcontext.writer.VariantContextWriter in project jvarkit by lindenb.

the class VcfIndexTabix method doVcfToVcf.

private int doVcfToVcf(String inputName, final VcfIterator vcfIn, final File outFile) throws IOException {
    SortingVCFWriter sortingVCW = null;
    VariantContextWriterBuilder vcwb = new VariantContextWriterBuilder();
    VariantContextWriter w = null;
    try {
        SAMSequenceDictionary dict = vcfIn.getHeader().getSequenceDictionary();
        if (dict != null)
            vcwb.setReferenceDictionary(dict);
        vcwb.setOutputFile(outFile);
        vcwb.setOutputFileType(OutputType.BLOCK_COMPRESSED_VCF);
        w = vcwb.build();
        if (this.sort) {
            LOG.info("Creating a sorting writer");
            sortingVCW = new SortingVCFWriter(w);
            w = sortingVCW;
        }
        w.writeHeader(vcfIn.getHeader());
        SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(vcfIn.getHeader());
        while (vcfIn.hasNext()) {
            w.add(progress.watch(vcfIn.next()));
        }
        progress.finish();
        w.close();
        w = null;
        return RETURN_OK;
    } catch (Exception e) {
        if (outFile.exists() && outFile.isFile()) {
            LOG.warn("Deleting " + outFile);
            outFile.delete();
            File tbi = new File(outFile.getPath() + TabixUtils.STANDARD_INDEX_EXTENSION);
            if (tbi.exists() && tbi.isFile())
                tbi.delete();
        }
        LOG.error(e);
        return -1;
    } finally {
        CloserUtil.close(w);
    }
}

Example 64 with VariantContextWriter

use of htsjdk.variant.variantcontext.writer.VariantContextWriter in project jvarkit by lindenb.

the class VcfMultiToOneAllele method doVcfToVcf.

@Override
public 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 0;
}

Example 65 with VariantContextWriter

use of htsjdk.variant.variantcontext.writer.VariantContextWriter in project jvarkit by lindenb.

the class VcfRemoveUnusedAlt method doVcfToVcf.

@Override
protected int doVcfToVcf(final String inputName, final VcfIterator in, final VariantContextWriter delegate) {
    try {
        final VariantContextWriter out = this.component.open(delegate);
        out.writeHeader(in.getHeader());
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(in.getHeader()).logger(LOG);
        while (in.hasNext()) {
            out.add(progress.watch(in.next()));
        }
        progress.finish();
        out.close();
        return 0;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    }
}