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

Example 56 with Genotype

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

the class VcfStage method makeGenotypePie.

private PieChart makeGenotypePie(final VariantContext ctx) {
    final Counter<GenotypeType> countTypes = new Counter<>();
    if (ctx != null) {
        for (final Genotype g : ctx.getGenotypes()) {
            // ignore genotype if not displayed
            final SampleDef sampleDef = this.name2sampledef.get(g.getSampleName());
            if (sampleDef == null || !sampleDef.isDisplayed())
                continue;
            countTypes.incr(g.getType());
        }
    }
    final ObservableList<PieChart.Data> pieChartData = FXCollections.observableArrayList();
    for (final GenotypeType t : GenotypeType.values()) {
        int c = (int) countTypes.count(t);
        if (c == 0)
            continue;
        pieChartData.add(new PieChart.Data(t.name() + " = " + c, c));
    }
    final PieChart chart = new PieChart(pieChartData);
    chart.setLegendVisible(false);
    return chart;
}

Example 57 with Genotype

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

the class VcfStage method paintDrawingArea.

private void paintDrawingArea() {
    final double canvaswidth = this.drawingArea.getCanvas().getWidth();
    if (canvaswidth < 1)
        return;
    final double canvasheight = this.drawingArea.getCanvas().getHeight();
    if (canvasheight < 1)
        return;
    final GraphicsContext gc = this.drawingArea.getCanvas().getGraphicsContext2D();
    gc.setGlobalAlpha(1.0);
    gc.setFill(Color.WHITE);
    gc.fillRect(0, 0, canvaswidth, canvasheight);
    if (this.variantTable.getItems().isEmpty())
        return;
    gc.setFill(Color.BLACK);
    final int MAX_VARIANTS = (int) (canvaswidth / 4.0);
    if (this.variantTable.getItems().size() > MAX_VARIANTS) {
        gc.setFont(Font.font("Verdana", 24));
        gc.fillText("Sorry. Too Many Variants (N=" + this.variantTable.getItems().size() + ">" + MAX_VARIANTS + ")", 2, 50);
        return;
    }
    // genome track
    int nrows = 1;
    for (final SampleDef sampleDef : this.name2sampledef.values()) {
        if (!sampleDef.isDisplayed())
            continue;
        nrows++;
    }
    double rowheight = canvasheight / nrows;
    if (rowheight < 5)
        rowheight = 5;
    // no margin if no sample
    final double marginleft = (nrows <= 1 ? 0.0 : canvaswidth / 10.0);
    final Function<Long, Double> convertGenomicIndexToPixel;
    final Function<Integer, Double> convertListIndexToPixel;
    if (!this.canvasEvenlySpaced.isSelected()) {
        Long minGenomicIndex;
        Long maxGenomicIndex;
        {
            final VariantContext ctx = this.variantTable.getItems().get(0);
            minGenomicIndex = convertContigPosToGenomicIndex(ctx.getContig(), ctx.getStart());
            maxGenomicIndex = minGenomicIndex;
        }
        {
            final VariantContext ctx = this.variantTable.getItems().get(this.variantTable.getItems().size() - 1);
            maxGenomicIndex = convertContigPosToGenomicIndex(ctx.getContig(), ctx.getEnd());
        }
        if (minGenomicIndex == null || maxGenomicIndex == null)
            return;
        long extend = (long) ((maxGenomicIndex - minGenomicIndex) * 0.1);
        minGenomicIndex = minGenomicIndex - extend;
        maxGenomicIndex = maxGenomicIndex + extend;
        final long genomicIndexStart = minGenomicIndex;
        final long genomicIndexLength = (maxGenomicIndex - minGenomicIndex);
        convertGenomicIndexToPixel = (GI) -> {
            double x = marginleft + (canvaswidth - marginleft) * ((double) (GI - genomicIndexStart)) / ((double) (genomicIndexLength));
            return x;
        };
        convertListIndexToPixel = null;
    } else {
        final double nItems = 2.0 + this.variantTable.getItems().size();
        convertGenomicIndexToPixel = null;
        convertListIndexToPixel = (IDX) -> {
            return marginleft + ((1 + IDX) / nItems) * (canvaswidth - marginleft);
        };
    }
    // draw vertical lines
    String prev_chr = "";
    Paint fill_chr1 = Color.BLACK;
    Paint fill_chr2 = Color.DARKGRAY;
    Paint fill_current = fill_chr1;
    gc.setFont(Font.font("Verdana", 7));
    for (int idx = 0; idx < this.variantTable.getItems().size(); ++idx) {
        final VariantContext ctx = this.variantTable.getItems().get(idx);
        if (!ctx.getContig().equals(prev_chr)) {
            prev_chr = ctx.getContig();
            fill_current = (fill_current == fill_chr1 ? fill_chr2 : fill_chr1);
        }
        gc.setFill(fill_current);
        double x0;
        double x1;
        if (convertListIndexToPixel == null) {
            x0 = convertGenomicIndexToPixel.apply(convertContigPosToGenomicIndex(ctx.getContig(), ctx.getStart()));
            x1 = convertGenomicIndexToPixel.apply(convertContigPosToGenomicIndex(ctx.getContig(), ctx.getEnd()));
            if (x0 <= x1)
                x1 = x0 + 1;
        } else {
            x0 = convertListIndexToPixel.apply(idx);
            x1 = x0 + 1;
        }
        gc.setGlobalAlpha(0.4);
        gc.fillRect(x0, 0, (x1 - x0), canvasheight);
        // http://stackoverflow.com/questions/39524792/
        gc.setGlobalAlpha(1.0);
        gc.setFill(Color.BLACK);
        gc.save();
        gc.translate(x0, 0);
        gc.rotate(90);
        gc.fillText(ctx.getContig() + ":" + ctx.getStart(), 5, 0, rowheight);
        gc.restore();
    }
    final double radius = 3.0;
    gc.setFont(Font.font("Verdana", 12));
    double y = rowheight;
    for (final SampleDef sampleDef : this.name2sampledef.values()) {
        if (!sampleDef.isDisplayed())
            continue;
        gc.setLineWidth(1.0);
        gc.setGlobalAlpha(1.0);
        gc.setFill(Color.BLACK);
        gc.setStroke(Color.BLACK);
        gc.strokeLine(0, y, canvaswidth, y);
        gc.fillText(sampleDef.getName(), 1, y + gc.getFont().getSize(), marginleft);
        gc.setLineWidth(0.5);
        final double midy = y + rowheight / 2.0;
        gc.setGlobalAlpha(0.8);
        for (int idx = 0; idx < this.variantTable.getItems().size(); ++idx) {
            final VariantContext ctx = this.variantTable.getItems().get(idx);
            double x0;
            if (convertListIndexToPixel == null) {
                x0 = convertGenomicIndexToPixel.apply(convertContigPosToGenomicIndex(ctx.getContig(), ctx.getStart()));
            } else {
                x0 = convertListIndexToPixel.apply(idx);
            }
            final Genotype g = ctx.getGenotype(sampleDef.getName());
            if (g == null || g.isNoCall())
                continue;
            if (g.isHomRef()) {
                gc.setStroke(Color.DARKGRAY);
                gc.strokeOval(x0 - radius, midy - radius, radius * 2, radius * 2);
            } else if (g.isHet() && !g.isHetNonRef()) {
                gc.setStroke(Color.DARKGRAY);
                gc.strokeOval(x0 - radius, midy - radius, radius * 2, radius * 2);
                gc.setFill(Color.RED);
                gc.fillArc(x0 - radius, midy - radius, radius * 2, radius * 2, 0, 180, ArcType.CHORD);
            } else if (g.isHetNonRef()) {
                gc.setFill(Color.PINK);
                gc.fillOval(x0 - radius, midy - radius, radius * 2, radius * 2);
                gc.setFill(Color.RED);
                gc.fillArc(x0 - radius, midy - radius, radius * 2, radius * 2, 0, 180, ArcType.CHORD);
            } else {
                gc.setFill(Color.RED);
                gc.fillOval(x0 - radius, midy - radius, radius * 2, radius * 2);
            }
        }
        y += rowheight;
        if (y > canvasheight)
            break;
    }
}

Example 58 with Genotype

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

the class VcfStage method buildTrioTable.

/**
 * build Trio table
 */
private TableView<PedFile.TrioGenotype> buildTrioTable() {
    final TableView<PedFile.TrioGenotype> table = new TableView<>();
    if (getVcfFile().getHeader().getNGenotypeSamples() > 0 && !getPedigree().isEmpty()) {
        final Function<Genotype, String> gt2str = new Function<Genotype, String>() {

            @Override
            public String apply(final Genotype gt) {
                if (gt == null || !gt.isCalled())
                    return null;
                return gt.getAlleles().stream().map(S -> allele2stringConverter.apply(S)).collect(Collectors.joining(gt.isPhased() ? "|" : "/"));
            }
        };
        table.getColumns().add(makeColumn("Child", T -> T.getChildren() == null ? null : T.getChildren().getSampleName()));
        table.getColumns().add(makeColumn("Child-GT", T -> gt2str.apply(T.getChildren())));
        table.getColumns().add(makeColumn("Father", T -> T.getFather() == null ? null : T.getFather().getSampleName()));
        table.getColumns().add(makeColumn("Father-GT", T -> gt2str.apply(T.getFather())));
        table.getColumns().add(makeColumn("Mother", T -> T.getMother() == null ? null : T.getMother().getSampleName()));
        table.getColumns().add(makeColumn("Mother-GT", T -> gt2str.apply(T.getMother())));
        table.getColumns().add(makeColumn("Violation", T -> T.isMendelianIncompatibility()));
    }
    table.setPlaceholder(new Label("No Trio."));
    return table;
}

Example 59 with Genotype

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

the class AFBySexChartFactory method visit.

@Override
public void visit(final VariantContext ctx) {
    for (final Allele alt : ctx.getAlternateAlleles()) {
        final MafCalculator[] mafCalculators = new MafCalculator[PedFile.Sex.values().length];
        for (int i = 0; i < mafCalculators.length; ++i) {
            mafCalculators[i] = new MafCalculator(alt, ctx.getContig());
        }
        for (final Genotype gt : ctx.getGenotypes()) {
            final PedFile.Sample sample = getPedigree().get(gt.getSampleName());
            if (sample == null) {
                mafCalculators[PedFile.Sex.Unknown.ordinal()].add(gt, false);
            } else {
                mafCalculators[sample.getSex().ordinal()].add(gt, sample.isMale());
            }
        }
        for (int i = 0; i < mafCalculators.length; ++i) {
            if (mafCalculators[i].isEmpty())
                continue;
            final Total total = popcount.get(i);
            total.num_maf++;
            total.sum += mafCalculators[i].getMaf();
        }
    }
}

Example 60 with Genotype

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

the class VcfToSql method read.

private void read(File filename) throws IOException {
    /* insert ATGC */
    this.alleleTable.insert(outputWriter, null, "A");
    this.alleleTable.insert(outputWriter, null, "C");
    this.alleleTable.insert(outputWriter, null, "G");
    this.alleleTable.insert(outputWriter, null, "T");
    /* insert this sample */
    this.vcfFileTable.insert(outputWriter, null, filename);
    final SelectStmt vcffile_id = new SelectStmt(this.vcfFileTable);
    final Map<String, SelectStmt> sample2sampleid = new HashMap<String, SelectStmt>();
    final Map<String, SelectStmt> filter2filterid = new HashMap<String, SelectStmt>();
    final Map<String, SelectStmt> chrom2chromId = new HashMap<String, SelectStmt>();
    final VcfIterator r = VCFUtils.createVcfIteratorFromFile(filename);
    final VCFHeader header = r.getHeader();
    /* parse samples */
    for (final String sampleName : header.getSampleNamesInOrder()) {
        this.sampleTable.insert(outputWriter, null, sampleName);
        SelectStmt sample_id = new SelectStmt(this.sampleTable, "name", sampleName);
        sample2sampleid.put(sampleName, sample_id);
        this.sample2fileTable.insert(outputWriter, null, vcffile_id, sample_id);
    }
    /* parse filters */
    for (final VCFFilterHeaderLine filter : header.getFilterLines()) {
        this.filterTable.insert(outputWriter, null, vcffile_id, filter.getID(), filter.getValue());
        filter2filterid.put(filter.getID(), new SelectStmt(this.filterTable, "name", filter.getID()));
    }
    filter2filterid.put(VCFConstants.PASSES_FILTERS_v4, new SelectStmt(this.filterTable, "name", VCFConstants.PASSES_FILTERS_v4));
    final SAMSequenceDictionary dict = header.getSequenceDictionary();
    if (dict == null) {
        throw new RuntimeException("dictionary missing in VCF");
    }
    /* parse sequence dict */
    for (final SAMSequenceRecord ssr : dict.getSequences()) {
        this.chromosomeTable.insert(outputWriter, null, vcffile_id, ssr.getSequenceName(), ssr.getSequenceLength());
        chrom2chromId.put(ssr.getSequenceName(), new SelectStmt(this.chromosomeTable, "name", ssr.getSequenceName()));
    }
    VepPredictionParser vepPredictionParser = new VepPredictionParserFactory(header).get();
    SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(dict);
    int nVariants = 0;
    while (r.hasNext()) {
        if (this.outputWriter.checkError())
            break;
        VariantContext var = progress.watch(r.next());
        ++nVariants;
        /* insert ref allele */
        this.alleleTable.insert(outputWriter, null, var.getReference().getBaseString());
        /* insert variant */
        this.variantTable.insert(outputWriter, null, vcffile_id, nVariants, chrom2chromId.get(var.getContig()), var.getStart(), (var.hasID() ? var.getID() : null), new SelectStmt(this.alleleTable, "bases", var.getReference().getBaseString()), (var.hasLog10PError() ? var.getPhredScaledQual() : null));
        SelectStmt variant_id = new SelectStmt(variantTable);
        /* insert alternate alleles */
        for (Allele alt : var.getAlternateAlleles()) {
            /* insert alt allele */
            this.alleleTable.insert(outputWriter, null, alt.getBaseString());
            this.variant2altTable.insert(outputWriter, null, variant_id, new SelectStmt(this.alleleTable, "bases", alt.getBaseString()));
        }
        /* insert filters */
        for (final String filter : var.getFilters()) {
            if (filter2filterid.get(filter) == null) {
                throw new IOException("VCF Error: filter " + filter + " is not defined in the VCF header.");
            }
            this.variant2filters.insert(outputWriter, null, variant_id, filter2filterid.get(filter));
        }
        if (!this.ignore_info) {
            for (final VepPrediction pred : vepPredictionParser.getPredictions(var)) {
            /*
					vepPrediction.insert(
							outputWriter,
							null,
							variant_id,
							pred.getEnsemblGene(),
							pred.getEnsemblTranscript(),
							pred.getEnsemblProtein(),
							pred.getSymbol()
							);
					SelectStmt pred_id = new SelectStmt(vepPrediction);
			
					for(SequenceOntologyTree.Term t: pred.getSOTerms())
						{
						String term=t.getAcn().replace(':', '_');
						soTermTable.insert(
								outputWriter,
								null,
								term,
								t.getAcn()
								);//for bioportal compatibility
						SelectStmt term_id = new SelectStmt(soTermTable,"acn",term);
						
						vepPrediction2so.insert(
							outputWriter,
							null,
							pred_id,
							term_id
							);
						}
					*/
            }
        }
        /* insert genotypes */
        for (final String sampleName : sample2sampleid.keySet()) {
            final Genotype g = var.getGenotype(sampleName);
            if (!g.isAvailable() || g.isNoCall())
                continue;
            genotypeTable.insert(outputWriter, null, variant_id, sample2sampleid.get(sampleName), g.isCalled() ? new SelectStmt(this.alleleTable, "bases", g.getAllele(0).getBaseString()) : null, g.isCalled() ? new SelectStmt(this.alleleTable, "bases", g.getAllele(1).getBaseString()) : null, g.hasDP() ? g.getDP() : null, g.hasGQ() ? g.getGQ() : null);
        }
    }
    r.close();
}