Examples of VCFInfoHeaderLine

Examples of htsjdk.variant.vcf.VCFInfoHeaderLine

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    @Override
    public List<String> getKeyNames() { return Arrays.asList("ReadPosRankSum"); }

    @Override
    public List<VCFInfoHeaderLine> getDescriptions() {
        return Arrays.asList(new VCFInfoHeaderLine("ReadPosRankSum", 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"));
    }
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Examples of htsjdk.variant.vcf.VCFInfoHeaderLine

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    }

    @Override
    public List<VCFInfoHeaderLine> getDescriptions() {
        return Arrays.asList(
                new VCFInfoHeaderLine(CCC, 1, VCFHeaderLineType.Integer, "Number of called chromosomes"),
                new VCFInfoHeaderLine(NCC, 1, VCFHeaderLineType.Integer, "Number of no-called samples"),
                new VCFInfoHeaderLine(HWP, 1, VCFHeaderLineType.Float, "P value from test of Hardy Weinberg Equilibrium"),
                new VCFInfoHeaderLine(GQ_MEAN, 1, VCFHeaderLineType.Float, "Mean of all GQ values"),
                new VCFInfoHeaderLine(GQ_STDDEV, 1, VCFHeaderLineType.Float, "Standard deviation of all GQ values")
        );
    }
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Examples of htsjdk.variant.vcf.VCFInfoHeaderLine

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public class BaseQualityRankSumTest extends RankSumTest implements StandardAnnotation {
    @Override
    public List<String> getKeyNames() { return Arrays.asList("BaseQRankSum"); }

    @Override
    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("BaseQRankSum", 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities")); }
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Examples of htsjdk.variant.vcf.VCFInfoHeaderLine

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        return map;
    }

    public List<String> getKeyNames() { return Arrays.asList("HW"); }

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("HW", 1, VCFHeaderLineType.Float, "Phred-scaled p-value for Hardy-Weinberg violation")); }
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Examples of htsjdk.variant.vcf.VCFInfoHeaderLine

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    }

    // return the descriptions used for the VCF INFO meta field
    public List<String> getKeyNames() { return Arrays.asList(HI_CONF_DENOVO_KEY,LO_CONF_DENOVO_KEY); }

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(HI_CONF_DENOVO_KEY, 1, VCFHeaderLineType.String, "High confidence possible de novo mutation (GQ >= "+hi_GQ_threshold+" for all trio members)=[comma-delimited list of child samples]"),
            new VCFInfoHeaderLine(LO_CONF_DENOVO_KEY, 1, VCFHeaderLineType.String, "Low confidence possible de novo mutation (GQ >= "+lo_GQ_threshold+" for child, GQ > 0 for parents)=[comma-delimited list of child samples]")); }
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Examples of htsjdk.variant.vcf.VCFInfoHeaderLine

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public class ClippingRankSumTest extends RankSumTest {
    @Override
    public List<String> getKeyNames() { return Arrays.asList("ClippingRankSum"); }

    @Override
    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("ClippingRankSum", 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases")); }
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Examples of htsjdk.variant.vcf.VCFInfoHeaderLine

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        return map;
    }

    public List<String> getKeyNames() { return Arrays.asList("Samples"); }

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("Samples", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "List of polymorphic samples")); }
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Examples of htsjdk.variant.vcf.VCFInfoHeaderLine

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public class MappingQualityRankSumTest extends RankSumTest implements StandardAnnotation {
    @Override
    public List<String> getKeyNames() { return Arrays.asList("MQRankSum"); }

    @Override
    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("MQRankSum", 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities")); }
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Examples of htsjdk.variant.vcf.VCFInfoHeaderLine

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            STATUS_KEY = null;

        // for now, INFO and FORMAT fields are not propagated to the output VCF (so they aren't put into the header)
        Set<VCFHeaderLine> headerLines = new HashSet<VCFHeaderLine>();
        if ( SET_KEY != null )
            headerLines.add(new VCFInfoHeaderLine(SET_KEY, 1, VCFHeaderLineType.String, "Source VCF for the merged record"));
        if ( STATUS_KEY != null )
            headerLines.add(new VCFInfoHeaderLine(STATUS_KEY, 1, VCFHeaderLineType.String, "Extent to which records match"));
        final VCFHeader vcfHeader = new VCFHeader(headerLines, Collections.<String>emptySet());
        baseWriter.writeHeader(vcfHeader);
        writer = VariantContextWriterFactory.sortOnTheFly(baseWriter, ACTIVE_WINDOW);
    }
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Examples of htsjdk.variant.vcf.VCFInfoHeaderLine

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    }

    public Set<VCFInfoHeaderLine> getAppropriateVCFInfoHeaders() {
        Set<VCFInfoHeaderLine> headerInfo = new HashSet<>();
        if ( configuration.genotypeArgs.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED )
            headerInfo.add(new VCFInfoHeaderLine(UnifiedGenotypingEngine.NUMBER_OF_DISCOVERED_ALLELES_KEY, 1, VCFHeaderLineType.Integer, "Number of alternate alleles discovered (but not necessarily genotyped) at this site"));
        return headerInfo;
    }
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