Package htsjdk.variant.vcf

Examples of htsjdk.variant.vcf.VCFFilterHeaderLine


        final List<String> inputNames = Arrays.asList(validation.getName());

        // setup the header fields
        Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
        hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames));
        hInfo.add(new VCFFilterHeaderLine("bootstrap","This site used for genotype bootstrapping with ProduceBeagleInputWalker"));

        bootstrapVCFOutput.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)));
    }
View Full Code Here


        final VCFFileReader in = new VCFFileReader(INPUT, false);
        final FilterApplyingVariantIterator iterator = new FilterApplyingVariantIterator(in.iterator(), variantFilters, genotypeFilters);

        final VariantContextWriter out = new VariantContextWriterBuilder().setOutputFile(OUTPUT).build();
        final VCFHeader header = in.getFileHeader();
        header.addMetaDataLine(new VCFFilterHeaderLine("AllGtsFiltered", "Site filtered out because all genotypes are filtered out."));
        header.addMetaDataLine(new VCFFormatHeaderLine("FT", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Genotype filters."));
        for (final VariantFilter filter : variantFilters) {
            for (final VCFFilterHeaderLine line : filter.headerLines()) {
                header.addMetaDataLine(line);
            }
View Full Code Here

        this.maxPhredScalePValue= maxPhredScalePValue;
    }

    @Override
    public List<VCFFilterHeaderLine> headerLines() {
        return CollectionUtil.makeList(new VCFFilterHeaderLine("StrandBias", "Site exhibits excessive allele/strand correlation."));
    }
View Full Code Here

        }
    }

    @Override
    public List<VCFFilterHeaderLine> headerLines() {
        return CollectionUtil.makeList(new VCFFilterHeaderLine(FILTER_NAME, "Site exhibits QD value below a hard limit."));
    }
View Full Code Here

    private static class Counts { int samples; int allele1; int allele2; }

    @Override
    public List<VCFFilterHeaderLine> headerLines() {
        return CollectionUtil.makeList(new VCFFilterHeaderLine(AB_FILTER, "Heterozygote allele balance below required threshold."));
    }
View Full Code Here

TOP

Related Classes of htsjdk.variant.vcf.VCFFilterHeaderLine

Copyright © 2018 www.massapicom. All rights reserved.
All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.