Examples with Genotype htsjdk.variant.variantcontext.Genotype used on opensource projects

Example 46 with Genotype

use of htsjdk.variant.variantcontext.Genotype in project hmftools by hartwigmedical.

the class StrelkaPostProcess method readAD.

@NotNull
private static int[] readAD(@NotNull final VariantContext variant, @NotNull Function<Allele, String> alleleKey) {
    final Genotype tumorGenotype = variant.getGenotype(TUMOR_GENOTYPE);
    final List<Integer> alleleAds = variant.getAlleles().stream().map(allele -> {
        final String[] alleleADs = tumorGenotype.getExtendedAttribute(alleleKey.apply(allele), "0").toString().split(SEPARATOR);
        if (alleleADs.length > 0) {
            try {
                return Integer.parseInt(alleleADs[0]);
            } catch (final NumberFormatException e) {
                return 0;
            }
        }
        return 0;
    }).collect(Collectors.toList());
    final Integer[] ads = new Integer[alleleAds.size()];
    return ArrayUtils.toPrimitive(alleleAds.toArray(ads));
}

Example 47 with Genotype

use of htsjdk.variant.variantcontext.Genotype in project hmftools by hartwigmedical.

the class MNVMerger method mergeVariants.

// MIVO: assumes variant list is sorted by start position and variants have only one sample (tumor)
// MIVO: gaps will *ALWAYS* be added to the output variant (no checking is done here to make sure they are needed)
@NotNull
@VisibleForTesting
static VariantContext mergeVariants(@NotNull final List<VariantContext> variants, @NotNull final Map<Integer, Character> gapReads) {
    final List<Allele> alleles = createMnvAlleles(variants, gapReads);
    final VariantContext firstVariant = variants.get(0);
    final VariantContext lastVariant = variants.get(variants.size() - 1);
    final Map<String, Object> attributes = createMnvAttributes(variants);
    final String sampleName = firstVariant.getSampleNamesOrderedByName().get(0);
    final Genotype genotype = new GenotypeBuilder(sampleName, alleles).DP(mergeDP(variants)).AD(mergeAD(variants)).make();
    return new VariantContextBuilder(firstVariant.getSource(), firstVariant.getContig(), firstVariant.getStart(), lastVariant.getEnd(), alleles).genotypes(genotype).filters(firstVariant.getFilters()).attributes(attributes).make();
}

Example 48 with Genotype

use of htsjdk.variant.variantcontext.Genotype in project ASCIIGenome by dariober.

the class GenotypeMatrix method genotypeAsAlleleIndexes.

/**
 * Get the sample genotype in the same format as it appears on the VCF file.
 * I.e. allele indexes separated by '/' or '|' (if phased). E.g. 0/0, 0/1 etc
 */
private String genotypeAsAlleleIndexes(VariantContext ctx, String sample) {
    Genotype gt = ctx.getGenotype(sample);
    char sep = gt.isPhased() ? '|' : '/';
    List<String> all = new ArrayList<String>();
    for (Allele a : gt.getAlleles()) {
        if (a.isNoCall()) {
            all.add(".");
        } else {
            int i = ctx.getAlleleIndex(a);
            all.add(Integer.toString(i));
        }
    }
    return '"' + Joiner.on(sep).join(all) + '"';
}

Example 49 with Genotype

use of htsjdk.variant.variantcontext.Genotype in project jvarkit by lindenb.

the class BamToSVG method printSample.

private void printSample(XMLStreamWriter w, double top_y, final Sample sample) throws XMLStreamException {
    w.writeComment("START SAMPLE: " + sample.name);
    w.writeStartElement(SVG.NS, "g");
    w.writeAttribute("transform", "translate(0," + top_y + ")");
    double y = 0;
    /* write title */
    w.writeEmptyElement("path");
    w.writeAttribute("class", "samplename");
    w.writeAttribute("title", sample.name);
    w.writeAttribute("d", this.hershey.svgPath(sample.name, scaleRect(new Rectangle2D.Double(0, y, this.drawinAreaWidth, HEIGHT_SAMPLE_NAME))));
    y += HEIGHT_SAMPLE_NAME;
    /* write REFERENCE */
    w.writeComment("REFERENCE");
    for (int pos = this.interval.start; // ignore if too small
    this.featureWidth > 5 && pos <= this.interval.end; ++pos) {
        char c = (this.genomicSequence == null ? 'N' : this.genomicSequence.charAt(pos - 1));
        double x0 = baseToPixel(pos);
        w.writeEmptyElement("use");
        w.writeAttribute("x", format(x0));
        w.writeAttribute("y", format(y));
        w.writeAttribute("xlink", XLINK.NS, "href", "#b" + c);
    }
    y += featureHeight;
    /* skip line for later consensus */
    double consensus_y = y;
    y += featureHeight;
    Map<Integer, Counter<Character>> pos2consensus = new HashMap<Integer, Counter<Character>>();
    /* print variants */
    if (!pos2variant.isEmpty()) {
        for (VariantContext ctx : this.pos2variant) {
            Genotype g = ctx.getGenotype(sample.name);
            if (g == null || !g.isCalled() || g.isHomRef())
                continue;
            if (ctx.getEnd() < this.interval.start)
                continue;
            if (ctx.getStart() > this.interval.end)
                continue;
            double x0 = baseToPixel(ctx.getStart());
            w.writeEmptyElement("use");
            w.writeAttribute("x", format(x0));
            w.writeAttribute("y", format(y));
            w.writeAttribute("title", ctx.getAltAlleleWithHighestAlleleCount().getDisplayString());
            if (g.isHomVar()) {
                w.writeAttribute("xlink", XLINK.NS, "href", "#homvar");
            } else if (g.isHet()) {
                w.writeAttribute("xlink", XLINK.NS, "href", "#het");
            }
        }
        y += featureHeight;
    }
    /* print all lines */
    w.writeComment("Alignments");
    for (int nLine = 0; nLine < sample.lines.size(); ++nLine) {
        w.writeStartElement("g");
        w.writeAttribute("transform", "translate(0," + format(y + nLine * featureHeight) + ")");
        List<SAMRecord> line = sample.lines.get(nLine);
        // loop over records on that line
        for (SAMRecord record : line) {
            printSamRecord(w, record, pos2consensus);
        }
        // g
        w.writeEndElement();
    }
    /* write consensus */
    w.writeComment("Consensus");
    for (int pos = this.interval.start; // ignore if too small
    this.featureWidth > 5 && pos <= this.interval.end; ++pos) {
        Counter<Character> cons = pos2consensus.get(pos);
        if (cons == null)
            continue;
        char c = cons.getMostFrequent();
        double x0 = baseToPixel(pos);
        w.writeEmptyElement("use");
        w.writeAttribute("x", format(x0));
        w.writeAttribute("y", format(consensus_y));
        w.writeAttribute("xlink", XLINK.NS, "href", "#b" + c);
    }
    /* surrounding frame for that sample */
    w.writeEmptyElement("rect");
    w.writeAttribute("class", "frame");
    w.writeAttribute("x", format(0));
    w.writeAttribute("y", format(0));
    w.writeAttribute("width", format(drawinAreaWidth));
    w.writeAttribute("height", format(sample.getHeight()));
    // g for sample
    w.writeEndElement();
    w.writeComment("END SAMPLE: " + sample.name);
}

Example 50 with Genotype

use of htsjdk.variant.variantcontext.Genotype in project jvarkit by lindenb.

the class IgvReview method start.

@Override
public void start(final Stage stage) throws Exception {
    stage.setTitle(getClass().getSimpleName());
    Predicate<VariantContext> ctxFilter;
    Map<String, String> params = super.getParameters().getNamed();
    if (params.containsKey("--filter")) {
        ctxFilter = JexlVariantPredicate.create(params.get("--filter"));
    } else {
        ctxFilter = V -> true;
    }
    final List<String> args = super.getParameters().getUnnamed();
    final File configFile;
    if (args.isEmpty()) {
        final FileChooser fc = new FileChooser();
        final String lastDirStr = preferences.get(LAST_USED_DIR_KEY, null);
        if (lastDirStr != null && !lastDirStr.isEmpty()) {
            fc.setInitialDirectory(new File(lastDirStr));
        }
        fc.getExtensionFilters().addAll(Collections.singletonList(new FileChooser.ExtensionFilter("Config file", "*.config", "*.cfg", "*.list")));
        configFile = fc.showOpenDialog(stage);
    } else if (args.size() == 1) {
        configFile = new File(args.get(0));
    } else {
        configFile = null;
    }
    if (configFile == null || !configFile.exists()) {
        JfxUtils.dialog().cause("Illegal number of arguments or file doesn't exists.").show(stage);
        Platform.exit();
        return;
    }
    if (configFile.isFile() && configFile.getParentFile() != null) {
        this.preferences.put(LAST_USED_DIR_KEY, configFile.getParentFile().getPath());
    }
    final List<String> configLines = Files.readAllLines(configFile.toPath());
    final Predicate<String> ignoreComment = (S) -> !S.startsWith("#");
    final Predicate<String> predVcf = S -> S.endsWith(".vcf") || S.endsWith(".vcf.gz");
    if (configLines.stream().filter(ignoreComment).filter(predVcf).count() != 1) {
        JfxUtils.dialog().cause("Found more than one vcf file in " + configFile).show(stage);
        Platform.exit();
        return;
    }
    final File vcfFile = configLines.stream().filter(ignoreComment).filter(predVcf).map(S -> new File(S)).findFirst().get();
    LOG.info("Opening vcf file and loading in memory");
    VCFFileReader vfr = null;
    CloseableIterator<VariantContext> iter = null;
    final Set<String> sampleNames;
    try {
        this.variants.clear();
        vfr = new VCFFileReader(vcfFile, false);
        this.vcfHeader = vfr.getFileHeader();
        sampleNames = new HashSet<>(this.vcfHeader.getSampleNamesInOrder());
        if (sampleNames.isEmpty()) {
            JfxUtils.dialog().cause("No Genotypes in " + vcfFile).show(stage);
            Platform.exit();
            return;
        }
        iter = vfr.iterator();
        this.variants.addAll(iter.stream().filter(ctxFilter).filter(CTX -> CTX.isVariant()).collect(Collectors.toList()));
    } catch (final Exception err) {
        JfxUtils.dialog().cause(err).show(stage);
        Platform.exit();
        return;
    } finally {
        CloserUtil.close(iter);
        CloserUtil.close(vfr);
    }
    if (this.variants.isEmpty()) {
        JfxUtils.dialog().cause("No Variants").show(stage);
        Platform.exit();
        return;
    }
    final SAMSequenceDictionary dict = this.vcfHeader.getSequenceDictionary();
    if (dict == null || dict.isEmpty()) {
        JfxUtils.dialog().cause(JvarkitException.VcfDictionaryMissing.getMessage(vcfFile.getPath())).show(stage);
        Platform.exit();
        return;
    }
    final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.LENIENT);
    configLines.stream().filter(ignoreComment).filter(S -> S.endsWith(".bam")).map(S -> new File(S)).forEach(F -> {
        final SamReader samIn = srf.open(F);
        final SAMFileHeader header = samIn.getFileHeader();
        CloserUtil.close(samIn);
        String sample = null;
        for (final SAMReadGroupRecord rg : header.getReadGroups()) {
            String s = rg.getSample();
            if (s == null)
                continue;
            if (sample == null) {
                sample = s;
            } else if (!sample.equals(s)) {
                JfxUtils.dialog().cause("Two samples in " + F).show(stage);
                Platform.exit();
                return;
            }
        }
        if (sample == null) {
            JfxUtils.dialog().cause("No sample in " + F + ". Ignoring").show(stage);
            return;
        }
        if (!sampleNames.contains(sample)) {
            JfxUtils.dialog().cause("Not in VCF header " + sample + " / " + F + ". Ignoring").show(stage);
            return;
        }
        this.sample2bamFile.put(sample, F);
    });
    if (this.sample2bamFile.isEmpty()) {
        JfxUtils.dialog().cause("No valid bam file in " + configFile).show(stage);
        return;
    }
    sampleNames.retainAll(this.sample2bamFile.keySet());
    if (sampleNames.isEmpty()) {
        JfxUtils.dialog().cause("No Sample associated to bam").show(stage);
        return;
    }
    ObservableList<VariantAndGenotype> genotypes = FXCollections.observableArrayList(this.variants.stream().flatMap(CTX -> CTX.getGenotypes().stream().filter(G -> sampleNames.contains(G.getSampleName())).map(G -> new VariantAndGenotype(CTX, G))).collect(Collectors.toList()));
    if (genotypes.isEmpty()) {
        JfxUtils.dialog().cause("No Genotype to show").show(stage);
        return;
    }
    Menu menu = new Menu("File");
    MenuItem menuItem = new MenuItem("Save as...");
    menuItem.setOnAction(AE -> {
        saveVariantsAs(stage);
    });
    menu.getItems().add(menuItem);
    menuItem = new MenuItem("Save");
    menuItem.setOnAction(AE -> {
        if (this.saveAsFile != null) {
            saveVariants(stage, this.saveAsFile);
        } else {
            saveVariantsAs(stage);
        }
    });
    menu.getItems().add(menuItem);
    menu.getItems().add(new SeparatorMenuItem());
    menuItem = new MenuItem("Quit");
    menuItem.setOnAction(AE -> {
        Platform.exit();
    });
    menu.getItems().add(menuItem);
    MenuBar bar = new MenuBar(menu);
    this.genotypeTable = new TableView<>(genotypes);
    this.genotypeTable.getColumns().add(makeColumn("CHROM", G -> G.ctx.getContig()));
    this.genotypeTable.getColumns().add(makeColumn("POS", G -> G.ctx.getStart()));
    this.genotypeTable.getColumns().add(makeColumn("ID", G -> G.ctx.getID()));
    this.genotypeTable.getColumns().add(makeColumn("REF", G -> G.ctx.getReference().getDisplayString()));
    this.genotypeTable.getColumns().add(makeColumn("ALT", G -> G.ctx.getAlternateAlleles().stream().map(A -> A.getDisplayString()).collect(Collectors.joining(","))));
    this.genotypeTable.getColumns().add(makeColumn("Sample", G -> G.g.getSampleName()));
    this.genotypeTable.getColumns().add(makeColumn("Type", G -> G.g.getType().name()));
    this.genotypeTable.getColumns().add(makeColumn("Alleles", G -> G.g.getAlleles().stream().map(A -> A.getDisplayString()).collect(Collectors.joining(","))));
    TableColumn<VariantAndGenotype, String> reviewCol = new TableColumn<>("Review");
    reviewCol.setCellValueFactory(C -> C.getValue().getReviewProperty());
    reviewCol.setCellFactory(TextFieldTableCell.forTableColumn());
    reviewCol.setOnEditCommit((E) -> {
        int y = E.getTablePosition().getRow();
        this.genotypeTable.getItems().get(y).setReview(E.getNewValue());
    });
    reviewCol.setEditable(true);
    this.genotypeTable.getColumns().add(reviewCol);
    this.genotypeTable.getSelectionModel().cellSelectionEnabledProperty().set(true);
    this.genotypeTable.setEditable(true);
    final ContextMenu cm = new ContextMenu();
    MenuItem mi1 = new MenuItem("Menu 1");
    cm.getItems().add(mi1);
    MenuItem mi2 = new MenuItem("Menu 2");
    cm.getItems().add(mi2);
    this.genotypeTable.setOnMousePressed(event -> {
        if (event.isPrimaryButtonDown() && (event.getClickCount() == 3 || event.isShiftDown())) {
            moveIgvTo(stage, genotypeTable.getSelectionModel().getSelectedItem());
        } else if (event.isSecondaryButtonDown()) {
            cm.show(genotypeTable, event.getScreenX(), event.getScreenY());
        }
    });
    final BorderPane pane2 = new BorderPane(this.genotypeTable);
    pane2.setPadding(new Insets(10, 10, 10, 10));
    VBox vbox1 = new VBox(bar, pane2);
    final Scene scene = new Scene(vbox1, 500, 300);
    stage.setScene(scene);
    stage.show();
}