Package htsjdk.variant.vcf

Examples of htsjdk.variant.vcf.VCFInfoHeaderLine

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        assertEquals(header0.getColumnCount(), header1.getColumnCount());
        assertEquals(header0.getGenotypeSamples(), header1.getGenotypeSamples());
        assertEquals(header0.getContigLines(), header1.getContigLines());

        for (VCFInfoHeaderLine line0 : header0.getInfoHeaderLines()) {
            VCFInfoHeaderLine line1 = header1.getInfoHeaderLine(line0.getID());
            assertEquals(line0.getCount(), line1.getCount());
            assertEquals(line0.getType(), line1.getType());
            assertEquals(line0.getDescription(), line1.getDescription());
            assertEquals(0, line0.compareTo(line1));
        }
    }
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        return Arrays.asList(FS);
    }

    public List<VCFInfoHeaderLine> getDescriptions() {
        return Arrays.asList(
            new VCFInfoHeaderLine(FS, 1, VCFHeaderLineType.Float, "Phred-scaled p-value using Fisher's exact test to detect strand bias"));
    }
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        return map;
    }

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

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("GC", 1, VCFHeaderLineType.Integer, "GC content within 20 bp +/- the variant")); }
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    }


    public List<String> getKeyNames() { return Arrays.asList("ABCI5","ABCI50","ABCI95"); }

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("ABCI5", 1, VCFHeaderLineType.Float, "Allele Balance lower 5% confidence interval"),
            new VCFInfoHeaderLine("ABCI50", 1, VCFHeaderLineType.Float, "Allele Balance middle 50% confidence interval"),
            new VCFInfoHeaderLine("ABCI95", 1, VCFHeaderLineType.Float, "Allele Balance upper 5% confidence interval")); }
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    }


    public List<String> getKeyNames() { return Arrays.asList("MPGHomRef","MPGHetRef","MPGHomVar","MPGLikHomRef","MPGLikHetRef","MPGLikHomVar"); }

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("MPGHomRef", 1, VCFHeaderLineType.Float, "Most Probable Genotype likelihood ratio for Hom Ref"),
            new VCFInfoHeaderLine("MPGHetRef", 1, VCFHeaderLineType.Float, "Most Probable Genotype likelihood ratio for Het Ref"),
            new VCFInfoHeaderLine("MPGHomVar", 1, VCFHeaderLineType.Float, "Most Probable Genotype likelihood ratio for Hom Var"),
            new VCFInfoHeaderLine("MPGLikHomRef", 1, VCFHeaderLineType.Float, "Raw likelihood for Hom Ref"),
            new VCFInfoHeaderLine("MPGLikHetRef", 1, VCFHeaderLineType.Float, "Raw likelihood for Het Ref"),
            new VCFInfoHeaderLine("MPGLikHomVar", 1, VCFHeaderLineType.Float, "Raw likelihood for Hom Var")); }
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    public List<String> getKeyNames() {
        return Arrays.asList("ReadMeanLen");
    }

    public List<VCFInfoHeaderLine> getDescriptions() {
        return Arrays.asList(new VCFInfoHeaderLine("ReadMeanLen", 1, VCFHeaderLineType.Float, "Mean number of aligned bases for reads - low number indicate possible mis-alignments"));
    }
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    public List<String> getKeyNames() {
        return Arrays.asList("ReadPosEndDist");
    }

    public List<VCFInfoHeaderLine> getDescriptions() {
        return Arrays.asList(new VCFInfoHeaderLine("ReadPosEndDist", 1, VCFHeaderLineType.Float, "Parameters indicating incorrect local alignments: 1. Mean distance from either end of read "));
    }
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    public List<String> getKeyNames() {
        return Arrays.asList("ReadMeanPos");
    }

    public List<VCFInfoHeaderLine> getDescriptions() {
        return Arrays.asList(new VCFInfoHeaderLine("ReadMeanPos", 1, VCFHeaderLineType.Float, "Parameters indicating incorrect local alignments: Mean position inside read as a fraction of aligned read length "));
    }
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        return Collections.singletonMap(SOR, value);
    }

    @Override
    public List<VCFInfoHeaderLine> getDescriptions() {
        return Collections.singletonList(new VCFInfoHeaderLine(SOR, 1, VCFHeaderLineType.Float, "Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"));
    }
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    private final static double JITTER_SIGMA = 3;

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

    public List<VCFInfoHeaderLine> getDescriptions() {
        return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Variant Confidence/Quality by Depth"));
    }
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Related Classes of htsjdk.variant.vcf.VCFInfoHeaderLine

  • bcbio.gatk.tools.walkers.annotator.FisherStrand
  • bcbio.gatk.tools.walkers.annotator.GCContent
  • bcbio.variation.annotate.AlleleBalanceConfidenceInterval
  • bcbio.variation.annotate.MostProbableGenotype
  • bcbio.variation.annotate.ReadMeanLen
  • bcbio.variation.annotate.ReadMeanPos
  • bcbio.variation.annotate.ReadPosEndDist
  • org.broad.igv.variant.vcf.VCFWriterTest
  • org.broadinstitute.gatk.tools.walkers.annotator.AlleleBalance
  • org.broadinstitute.gatk.tools.walkers.annotator.BaseCounts
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