Examples with GeneExtractorFactory com.github.lindenb.jvarkit.util.vcf.predictions.GeneExtractorFactory used on opensource projects

Example 1 with GeneExtractorFactory

use of com.github.lindenb.jvarkit.util.vcf.predictions.GeneExtractorFactory in project jvarkit by lindenb.

the class VcfGeneSplitter method run.

private int run(final List<String> args) {
    SortingCollection<KeyAndLine> sortingcollection = null;
    BufferedReader in = null;
    FileOutputStream fos = null;
    CloseableIterator<KeyAndLine> iter = null;
    ArchiveFactory archiveFactory = null;
    PrintWriter manifest = null;
    try {
        final Path tmpVcf = Files.createTempFile("tmp.", ".vcf.gz");
        archiveFactory = ArchiveFactory.open(this.outputFile);
        manifest = new PrintWriter(this.manifestFile == null ? new NullOuputStream() : IOUtils.openPathForWriting(manifestFile));
        manifest.println("#chrom\tstart\tend\tsplitter\tgene\tkey\tpath\tCount_Variants");
        in = super.openBufferedReader(oneFileOrNull(args));
        final VCFUtils.CodecAndHeader cah = VCFUtils.parseHeader(in);
        final GeneExtractorFactory geneExtractorFactory = new GeneExtractorFactory(cah.header);
        final List<GeneExtractorFactory.GeneExtractor> extractors = geneExtractorFactory.parse(this.extractorsNames);
        if (extractors.isEmpty()) {
            LOG.warn("No extractor defined!");
            return -1;
        }
        final VCFEncoder vcfEncoder = new VCFEncoder(cah.header, false, false);
        // read variants
        final ProgressFactory.Watcher<VariantContext> progess = ProgressFactory.newInstance().dictionary(cah.header).logger(LOG).build();
        String prevCtg = null;
        for (; ; ) {
            final String line = in.readLine();
            final VariantContext ctx = (line == null ? null : cah.codec.decode(line));
            if (ctx != null)
                progess.apply(ctx);
            if (this.ignoreFiltered && ctx.isFiltered())
                continue;
            if (ctx == null || !ctx.getContig().equals(prevCtg)) {
                if (sortingcollection != null) {
                    sortingcollection.doneAdding();
                    iter = sortingcollection.iterator();
                    final EqualRangeIterator<KeyAndLine> eqiter = new EqualRangeIterator<>(iter, (o1, o2) -> o1.keyAndGene.compareTo(o2.keyAndGene));
                    while (eqiter.hasNext()) {
                        final List<KeyAndLine> buffer = eqiter.next();
                        if (buffer.size() < this.min_number_of_ctx)
                            continue;
                        if (this.max_number_of_ctx > 0 && buffer.size() > this.max_number_of_ctx)
                            continue;
                        final KeyAndLine first = buffer.get(0);
                        final VariantContextWriter out = VCFUtils.createVariantContextWriterToPath(tmpVcf);
                        final VCFHeader header2 = addMetaData(new VCFHeader(cah.header));
                        header2.addMetaDataLine(new VCFHeaderLine("GtfFileSplitter.Name", String.valueOf(first.keyAndGene.key)));
                        header2.addMetaDataLine(new VCFHeaderLine("GtfFileSplitter.Gene", String.valueOf(first.keyAndGene.gene)));
                        out.writeHeader(header2);
                        int minPos = Integer.MAX_VALUE;
                        int maxPos = 0;
                        for (final KeyAndLine kl : buffer) {
                            final VariantContext ctx2 = cah.codec.decode(kl.ctx);
                            minPos = Math.min(ctx2.getStart(), minPos);
                            maxPos = Math.max(ctx2.getEnd(), maxPos);
                            out.add(ctx2);
                        }
                        out.close();
                        final String md5 = StringUtils.md5(prevCtg + ":" + first.splitter + ":" + first.keyAndGene.key);
                        final String filename = md5.substring(0, 2) + File.separatorChar + md5.substring(2) + File.separator + buffer.get(0).keyAndGene.key.replaceAll("[/\\:]", "_") + ".vcf.gz";
                        final OutputStream os = archiveFactory.openOuputStream(filename);
                        IOUtils.copyTo(tmpVcf, os);
                        os.flush();
                        os.close();
                        manifest.print(prevCtg);
                        manifest.print('\t');
                        manifest.print(minPos - 1);
                        manifest.print('\t');
                        manifest.print(maxPos);
                        manifest.print('\t');
                        manifest.print(first.splitter);
                        manifest.print('\t');
                        manifest.print(first.keyAndGene.gene);
                        manifest.print('\t');
                        manifest.print(first.keyAndGene.key);
                        manifest.print('\t');
                        manifest.print((archiveFactory.isTarOrZipArchive() ? "" : this.outputFile.toString() + File.separator) + filename);
                        manifest.print('\t');
                        manifest.println(buffer.size());
                    }
                    eqiter.close();
                    iter.close();
                }
                sortingcollection = null;
                if (ctx == null)
                    break;
                prevCtg = ctx.getContig();
            }
            for (final GeneExtractorFactory.GeneExtractor ex : extractors) {
                final Map<GeneExtractorFactory.KeyAndGene, Set<String>> gene2values = ex.apply(ctx);
                if (gene2values.isEmpty())
                    continue;
                for (final GeneExtractorFactory.KeyAndGene keyAndGene : gene2values.keySet()) {
                    final Set<String> values = gene2values.get(keyAndGene);
                    if (values.isEmpty())
                        continue;
                    final VariantContextBuilder vcb = new VariantContextBuilder(ctx);
                    vcb.rmAttribute(VepPredictionParser.getDefaultTag());
                    vcb.rmAttribute(AnnPredictionParser.getDefaultTag());
                    vcb.attribute(ex.getInfoTag(), new ArrayList<>(values));
                    if (sortingcollection == null) {
                        sortingcollection = SortingCollection.newInstance(KeyAndLine.class, new KeyAndLineCodec(), new KeyAndLineComparator2(), this.writingSortingCollection.getMaxRecordsInRam(), this.writingSortingCollection.getTmpPaths());
                        sortingcollection.setDestructiveIteration(true);
                    }
                    sortingcollection.add(new KeyAndLine(new KeyGene(keyAndGene.getKey(), keyAndGene.getGene()), ex.getName(), vcfEncoder.encode(vcb.make())));
                }
            }
        }
        progess.close();
        manifest.flush();
        manifest.close();
        archiveFactory.close();
        Files.deleteIfExists(tmpVcf);
        return RETURN_OK;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(iter);
        if (sortingcollection != null)
            sortingcollection.cleanup();
        CloserUtil.close(in);
        CloserUtil.close(fos);
        CloserUtil.close(manifest);
    }
}

Example 2 with GeneExtractorFactory

use of com.github.lindenb.jvarkit.util.vcf.predictions.GeneExtractorFactory in project jvarkit by lindenb.

the class VCFComposite method doVcfToVcf.

protected int doVcfToVcf(final String inputName, final VCFIterator iterin, final VariantContextWriter out) {
    final VCFHeader header = iterin.getHeader();
    if (!header.hasGenotypingData()) {
        LOG.error("No genotypes in " + inputName);
        return -1;
    }
    final GeneExtractorFactory geneExtractorFactory = new GeneExtractorFactory(header);
    final List<GeneExtractorFactory.GeneExtractor> extractors = geneExtractorFactory.parse(this.extractorsNames);
    if (extractors.isEmpty()) {
        LOG.error("no gene extractor found/defined.");
        return -1;
    }
    final Pedigree pedigree;
    try {
        final Set<String> sampleNames = new HashSet<>(header.getSampleNamesInOrder());
        final PedigreeParser pedParser = new PedigreeParser();
        pedigree = pedParser.parse(this.pedigreeFile);
        if (pedigree == null || pedigree.isEmpty()) {
            LOG.error("pedigree missing/empty");
            return -1;
        }
        this.affectedSamples.addAll(pedigree.getAffectedSamples());
        this.affectedSamples.removeIf(S -> !sampleNames.contains(S.getId()));
        if (this.affectedSamples.isEmpty()) {
            LOG.error("No Affected sample in pedigree. " + this.pedigreeFile + "/" + inputName);
            return -1;
        }
        this.unaffectedSamples.addAll(pedigree.getUnaffectedSamples());
        this.unaffectedSamples.removeIf(S -> !sampleNames.contains(S.getId()));
        if (pedigree.getUnaffectedSamples().isEmpty()) {
            LOG.error("No Unaffected sample in " + this.pedigreeFile + "/" + inputName);
            return -1;
        }
    } catch (final IOException err) {
        throw new RuntimeIOException(err);
    }
    header.addMetaDataLine(new VCFInfoHeaderLine(INFO_TAG, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Variant of VCFComposite"));
    if (!StringUtils.isBlank(this.filterNonCompositeTag)) {
        header.addMetaDataLine(new VCFFilterHeaderLine(this.filterNonCompositeTag, "Not a Variant fir VCFComposite"));
    }
    final SAMSequenceDictionary dict = header.getSequenceDictionary();
    final Comparator<String> contigCmp;
    if (dict == null || dict.isEmpty()) {
        contigCmp = (A, B) -> A.compareTo(B);
    } else {
        contigCmp = new ContigDictComparator(dict);
    }
    final Comparator<VariantContext> ctxComparator = (V1, V2) -> {
        int i = contigCmp.compare(V1.getContig(), V2.getContig());
        if (i != 0)
            return i;
        i = Integer.compare(V1.getStart(), V2.getStart());
        if (i != 0)
            return i;
        return V1.getReference().compareTo(V2.getReference());
    };
    final Comparator<VariantLine> variantLineComparator = (V1, V2) -> {
        final int i = ctxComparator.compare(V1.ctx, V2.ctx);
        if (i != 0)
            return i;
        return Long.compare(V1.id, V2.id);
    };
    long ID_GENERATOR = 0L;
    this.vcfDecoder = VCFUtils.createDefaultVCFCodec();
    this.vcfDecoder.setVCFHeader(header, VCFHeaderVersion.VCF4_2);
    this.vcfEncoder = new VCFEncoder(header, false, true);
    SortingCollection<GeneAndVariant> sorting = null;
    SortingCollection<VariantLine> outputSorter = null;
    try {
        LOG.info("reading variants and genes");
        /* Gene and variant sorter */
        sorting = SortingCollection.newInstance(GeneAndVariant.class, new GeneAndVariantCodec(), GeneAndVariant::compareGeneThenIndex, this.writingSortingCollection.getMaxRecordsInRam(), this.writingSortingCollection.getTmpPaths());
        sorting.setDestructiveIteration(true);
        /* Variant sorter */
        outputSorter = SortingCollection.newInstance(VariantLine.class, new VariantLineCodec(), variantLineComparator, this.writingSortingCollection.getMaxRecordsInRam(), this.writingSortingCollection.getTmpPaths());
        outputSorter.setDestructiveIteration(true);
        /* read input */
        while (iterin.hasNext()) {
            final VariantContext ctx = iterin.next();
            final VariantLine variantLine = new VariantLine(++ID_GENERATOR, ctx);
            if (!this.variantJexl.test(ctx)) {
                outputSorter.add(variantLine);
                continue;
            }
            if (!acceptVariant(ctx)) {
                outputSorter.add(variantLine);
                continue;
            }
            final Set<GeneIdentifier> geneKeys = new HashSet<>();
            extractors.stream().map(EX -> EX.apply(ctx)).flatMap(H -> H.keySet().stream()).forEach(KG -> {
                geneKeys.add(new GeneIdentifier(KG.getKey(), KG.getGene(), KG.getMethod().replace('/', '_')));
            });
            if (geneKeys.isEmpty()) {
                outputSorter.add(variantLine);
                continue;
            }
            for (final GeneIdentifier gk : geneKeys) {
                final GeneAndVariant gav = new GeneAndVariant(gk, variantLine);
                gav.gene.contig = ctx.getContig();
                sorting.add(gav);
            }
        }
        sorting.doneAdding();
        LOG.info("compile per gene");
        this.reportGeneWriter = (this.geneReportPath == null ? new PrintWriter(new NullOuputStream()) : IOUtils.openPathForPrintWriter(this.geneReportPath));
        this.reportGeneWriter.print("#CHROM");
        this.reportGeneWriter.print('\t');
        this.reportGeneWriter.print("bed.start");
        this.reportGeneWriter.print('\t');
        this.reportGeneWriter.print("bed.end");
        this.reportGeneWriter.print('\t');
        this.reportGeneWriter.print("gene.key");
        this.reportGeneWriter.print('\t');
        this.reportGeneWriter.print("gene.label");
        this.reportGeneWriter.print('\t');
        this.reportGeneWriter.print("gene.source");
        this.reportGeneWriter.print('\t');
        this.reportGeneWriter.print("count.variants");
        this.reportGeneWriter.print('\t');
        this.reportGeneWriter.print("affected.counts");
        this.reportGeneWriter.print('\t');
        this.reportGeneWriter.print("affected.total");
        this.reportGeneWriter.print('\t');
        this.reportGeneWriter.print("affected.samples");
        this.reportGeneWriter.println();
        this.reportWriter = (this.reportPath == null ? new PrintWriter(new NullOuputStream()) : IOUtils.openPathForPrintWriter(this.reportPath));
        this.reportWriter.print("#CHROM");
        this.reportWriter.print('\t');
        this.reportWriter.print("bed.start");
        this.reportWriter.print('\t');
        this.reportWriter.print("bed.end");
        this.reportWriter.print('\t');
        this.reportWriter.print("gene.index");
        this.reportWriter.print('\t');
        this.reportWriter.print("gene.key");
        this.reportWriter.print('\t');
        this.reportWriter.print("gene.label");
        this.reportWriter.print('\t');
        this.reportWriter.print("gene.source");
        for (int side = 0; side < 2; ++side) {
            this.reportWriter.print('\t');
            final String prefix = "variant" + (side + 1) + ".";
            this.reportWriter.print(prefix + "start");
            this.reportWriter.print('\t');
            this.reportWriter.print(prefix + "end");
            this.reportWriter.print('\t');
            this.reportWriter.print(prefix + "ref");
            this.reportWriter.print('\t');
            this.reportWriter.print(prefix + "alt");
            this.reportWriter.print('\t');
            this.reportWriter.print(prefix + "info");
            for (final Sample sn : this.affectedSamples) {
                this.reportWriter.print('\t');
                this.reportWriter.print(prefix + "gt[" + sn.getId() + "].affected");
            }
            for (final Sample sn : this.unaffectedSamples) {
                this.reportWriter.print('\t');
                this.reportWriter.print(prefix + "gt[" + sn.getId() + "].unaffected");
            }
        }
        this.reportWriter.println();
        // compile data
        CloseableIterator<GeneAndVariant> iter2 = sorting.iterator();
        EqualRangeIterator<GeneAndVariant> eqiter = new EqualRangeIterator<>(iter2, (A, B) -> A.gene.compareTo(B.gene));
        while (eqiter.hasNext()) {
            final List<GeneAndVariant> variants = eqiter.next();
            scan(variants.get(0).gene, variants.stream().map(L -> L.variant).collect(Collectors.toList()));
            for (final GeneAndVariant ga : variants) outputSorter.add(ga.variant);
        }
        eqiter.close();
        iter2.close();
        sorting.cleanup();
        // 
        this.reportWriter.flush();
        this.reportWriter.close();
        this.reportGeneWriter.flush();
        this.reportGeneWriter.close();
        LOG.info("write variants");
        CloseableIterator<VariantLine> iter1 = outputSorter.iterator();
        EqualRangeIterator<VariantLine> eqiter1 = new EqualRangeIterator<>(iter1, variantLineComparator);
        out.writeHeader(header);
        while (eqiter1.hasNext()) {
            final List<VariantLine> array = eqiter1.next();
            final VariantContext firstCtx = array.get(0).ctx;
            final Set<String> set = getAnnotationsForVariant(firstCtx);
            final VariantContext outCtx;
            final VariantContextBuilder vcb = new VariantContextBuilder(firstCtx);
            for (int y = 1; y < array.size(); ++y) {
                set.addAll(getAnnotationsForVariant(array.get(y).ctx));
            }
            if (set.isEmpty()) {
                if (StringUtils.isBlank(this.filterNonCompositeTag)) {
                    // ignore
                    continue;
                } else {
                    vcb.filter(this.filterNonCompositeTag);
                }
            } else {
                if (!firstCtx.isFiltered()) {
                    vcb.passFilters();
                }
                vcb.attribute(INFO_TAG, new ArrayList<>(set));
            }
            outCtx = vcb.make();
            out.add(outCtx);
        }
        outputSorter.cleanup();
        eqiter1.close();
        iter1.close();
        return 0;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    }
}

Example 3 with GeneExtractorFactory

use of com.github.lindenb.jvarkit.util.vcf.predictions.GeneExtractorFactory in project jvarkit by lindenb.

the class GroupByGene method read.

private void read(final String input) throws IOException {
    SortingCollection<Call> sortingCollection = null;
    VCFIterator vcfIterator = null;
    try {
        final BcfIteratorBuilder iterbuilder = new BcfIteratorBuilder();
        vcfIterator = (input == null ? iterbuilder.open(stdin()) : iterbuilder.open(input));
        final VCFHeader header = vcfIterator.getHeader();
        this.contigDictComparator = new ContigDictComparator(SequenceDictionaryUtils.extractRequired(header));
        sortingCollection = SortingCollection.newInstance(Call.class, new CallCodec(header), (C1, C2) -> C1.compare2(C2), this.writingSortingCollection.getMaxRecordsInRam(), this.writingSortingCollection.getTmpPaths());
        sortingCollection.setDestructiveIteration(true);
        final GeneExtractorFactory geneExtractorFactory = new GeneExtractorFactory(header);
        final List<GeneExtractorFactory.GeneExtractor> geneExtractors = geneExtractorFactory.parse(this.extractorsNames);
        final List<String> sampleNames;
        if (header.getSampleNamesInOrder() != null) {
            sampleNames = header.getSampleNamesInOrder();
        } else {
            sampleNames = Collections.emptyList();
        }
        final Pedigree pedigree;
        if (this.pedigreePath != null) {
            final PedigreeParser pedParser = new PedigreeParser();
            pedigree = pedParser.parse(this.pedigreePath);
        } else {
            pedigree = PedigreeParser.empty();
        }
        final ProgressFactory.Watcher<VariantContext> progress = ProgressFactory.newInstance().dictionary(header).logger(LOG).build();
        while (vcfIterator.hasNext()) {
            final VariantContext ctx = progress.apply(vcfIterator.next());
            if (!ctx.isVariant())
                continue;
            if (ignore_filtered && ctx.isFiltered())
                continue;
            // simplify line
            final VariantContextBuilder vcb = new VariantContextBuilder(ctx);
            vcb.noID();
            vcb.log10PError(VariantContext.NO_LOG10_PERROR);
            vcb.unfiltered();
            vcb.attributes(Collections.emptyMap());
            final VariantContext ctx2 = vcb.make();
            final SortingCollection<Call> finalSorter = sortingCollection;
            geneExtractors.stream().flatMap(EX -> EX.apply(ctx).keySet().stream()).forEach(KG -> {
                final Call c = new Call();
                c.ctx = ctx2;
                c.gene = new GeneName(KG.getKey(), KG.getGene(), KG.getMethod());
                finalSorter.add(c);
            });
        }
        CloserUtil.close(vcfIterator);
        vcfIterator = null;
        sortingCollection.doneAdding();
        progress.close();
        /**
         * dump
         */
        final Set<String> casesSamples = pedigree.getAffectedSamples().stream().map(P -> P.getId()).filter(ID -> sampleNames.contains(ID)).collect(Collectors.toSet());
        final Set<String> controlsSamples = pedigree.getUnaffectedSamples().stream().map(P -> P.getId()).filter(ID -> sampleNames.contains(ID)).collect(Collectors.toSet());
        final Set<String> maleSamples = pedigree.getSamples().stream().filter(P -> P.isMale()).map(P -> P.getId()).filter(ID -> sampleNames.contains(ID)).collect(Collectors.toSet());
        final Set<String> femaleSamples = pedigree.getSamples().stream().filter(P -> P.isFemale()).map(P -> P.getId()).filter(ID -> sampleNames.contains(ID)).collect(Collectors.toSet());
        final Predicate<Genotype> genotypeFilter = genotype -> {
            if (!genotype.isAvailable())
                return false;
            if (!genotype.isCalled())
                return false;
            if (genotype.isNoCall())
                return false;
            if (genotype.isHomRef())
                return false;
            if (this.ignore_filtered_genotype && genotype.isFiltered())
                return false;
            return true;
        };
        PrintStream pw = openPathOrStdoutAsPrintStream(this.outFile);
        pw.print("#chrom");
        pw.print('\t');
        pw.print("min.POS");
        pw.print('\t');
        pw.print("max.POS");
        pw.print('\t');
        pw.print("gene.name");
        pw.print('\t');
        pw.print("gene.label");
        pw.print('\t');
        pw.print("gene.type");
        pw.print('\t');
        pw.print("samples.affected");
        pw.print('\t');
        pw.print("count.variations");
        if (this.print_positions) {
            pw.print('\t');
            pw.print("positions");
        }
        if (!casesSamples.isEmpty()) {
            pw.print('\t');
            pw.print("pedigree.cases");
        }
        if (!controlsSamples.isEmpty()) {
            pw.print('\t');
            pw.print("pedigree.controls");
        }
        if (!maleSamples.isEmpty()) {
            pw.print('\t');
            pw.print("pedigree.males");
        }
        if (!femaleSamples.isEmpty()) {
            pw.print('\t');
            pw.print("pedigree.females");
        }
        if (this.print_fisher && !controlsSamples.isEmpty() && !casesSamples.isEmpty()) {
            pw.print('\t');
            pw.print("fisher");
        }
        for (final String sample : sampleNames) {
            pw.print('\t');
            pw.print(sample);
        }
        pw.println();
        final CloseableIterator<Call> iter = sortingCollection.iterator();
        final EqualRangeIterator<Call> eqiter = new EqualRangeIterator<>(iter, (C1, C2) -> C1.compareTo(C2));
        while (eqiter.hasNext()) {
            final List<Call> row = eqiter.next();
            final Call first = row.get(0);
            final List<VariantContext> variantList = row.stream().map(R -> R.ctx).collect(Collectors.toList());
            final int minPos = variantList.stream().mapToInt(R -> R.getStart()).min().getAsInt();
            final int maxPos = variantList.stream().mapToInt(R -> R.getEnd()).max().getAsInt();
            final Set<String> sampleCarryingMut = new HashSet<String>();
            final Counter<String> pedCasesCarryingMut = new Counter<String>();
            final Counter<String> pedCtrlsCarryingMut = new Counter<String>();
            final Counter<String> malesCarryingMut = new Counter<String>();
            final Counter<String> femalesCarryingMut = new Counter<String>();
            final Counter<String> sample2count = new Counter<String>();
            for (final VariantContext ctx : variantList) {
                for (final Genotype genotype : ctx.getGenotypes()) {
                    if (!genotypeFilter.test(genotype))
                        continue;
                    final String sampleName = genotype.getSampleName();
                    sample2count.incr(sampleName);
                    sampleCarryingMut.add(sampleName);
                    if (casesSamples.contains(sampleName)) {
                        pedCasesCarryingMut.incr(sampleName);
                    }
                    if (controlsSamples.contains(sampleName)) {
                        pedCtrlsCarryingMut.incr(sampleName);
                    }
                    if (maleSamples.contains(sampleName)) {
                        malesCarryingMut.incr(sampleName);
                    }
                    if (femaleSamples.contains(sampleName)) {
                        femalesCarryingMut.incr(sampleName);
                    }
                }
            }
            pw.print(first.getContig());
            pw.print('\t');
            // convert to bed
            pw.print(minPos - 1);
            pw.print('\t');
            pw.print(maxPos);
            pw.print('\t');
            pw.print(first.gene.name);
            pw.print('\t');
            pw.print(first.gene.label);
            pw.print('\t');
            pw.print(first.gene.type);
            pw.print('\t');
            pw.print(sampleCarryingMut.size());
            pw.print('\t');
            pw.print(variantList.size());
            if (this.print_positions) {
                pw.print('\t');
                pw.print(variantList.stream().map(CTX -> String.valueOf(CTX.getStart()) + ":" + CTX.getAlleles().stream().map(A -> A.getDisplayString()).collect(Collectors.joining("/"))).collect(Collectors.joining(";")));
            }
            if (!casesSamples.isEmpty()) {
                pw.print('\t');
                pw.print(pedCasesCarryingMut.getCountCategories());
            }
            if (!controlsSamples.isEmpty()) {
                pw.print('\t');
                pw.print(pedCtrlsCarryingMut.getCountCategories());
            }
            if (!maleSamples.isEmpty()) {
                pw.print('\t');
                pw.print(malesCarryingMut.getCountCategories());
            }
            if (!femaleSamples.isEmpty()) {
                pw.print('\t');
                pw.print(femalesCarryingMut.getCountCategories());
            }
            if (this.print_fisher && !controlsSamples.isEmpty() && !casesSamples.isEmpty()) {
                int count_case_mut = 0;
                int count_ctrl_mut = 0;
                int count_case_wild = 0;
                int count_ctrl_wild = 0;
                for (final String sampleName : header.getSampleNamesInOrder()) {
                    final boolean has_mutation = variantList.stream().map(V -> V.getGenotype(sampleName)).anyMatch(G -> G != null && genotypeFilter.test(G));
                    if (controlsSamples.contains(sampleName)) {
                        if (has_mutation) {
                            count_ctrl_mut++;
                        } else {
                            count_ctrl_wild++;
                        }
                    } else if (casesSamples.contains(sampleName)) {
                        if (has_mutation) {
                            count_case_mut++;
                        } else {
                            count_case_wild++;
                        }
                    }
                }
                final FisherExactTest fisher = FisherExactTest.compute(count_case_mut, count_case_wild, count_ctrl_mut, count_ctrl_wild);
                pw.print('\t');
                pw.print(fisher.getAsDouble());
            }
            for (final String sample : sampleNames) {
                pw.print('\t');
                pw.print(sample2count.count(sample));
            }
            pw.println();
            if (pw.checkError())
                break;
        }
        eqiter.close();
        iter.close();
        pw.flush();
        if (this.outFile != null)
            pw.close();
    } finally {
        CloserUtil.close(vcfIterator);
        if (sortingCollection != null)
            sortingCollection.cleanup();
    }
}