/** Add POPMAX name */ private void addPopmaxHeader(VCFHeader header, String prefix, String idInfix, String noteInfix) { VCFInfoHeaderLine line = new VCFInfoHeaderLine(prefix + idInfix + "POPMAX", VCFHeaderLineCount.A, VCFHeaderLineType.String, "Population with the max AF" + noteInfix); header.addMetaDataLine(line); }
/** Add header for highest allele frequency */ private void addBestAFHeader(VCFHeader header, String prefix, String idInfix, String noteInfix) { VCFInfoHeaderLine line = new VCFInfoHeaderLine(prefix + idInfix + "AF_POPMAX", VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Highest allele frequency seen in any population" + noteInfix); header.addMetaDataLine(line); }
/** Add header for allele count with highest frequency */ private void addBestACHeader(VCFHeader header, String prefix, String idInfix, String noteInfix) { VCFInfoHeaderLine line = new VCFInfoHeaderLine(prefix + idInfix + "AC_POPMAX", VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Allele count for population with highest frequency" + noteInfix); header.addMetaDataLine(line); }
@Test(expectedExceptions = { IllegalArgumentException.class }, expectedExceptionsMessageRegExp = "Invalid count number, with fixed count the number should be 1 or higher: .*") public void testInfoNumberExeptions() { new VCFInfoHeaderLine("test", 0, VCFHeaderLineType.Integer, ""); }
@Test public void testNumberExceptionFlag() { // Should not raise an exception new VCFInfoHeaderLine("test", 0, VCFHeaderLineType.Flag, ""); } }
@Test public void supportsVersionFields() { final String line = "<ID=FOO,Number=1,Type=Float,Description=\"foo\",Version=3>"; final VCFCompoundHeaderLine headerline = new VCFInfoHeaderLine(line, VCFHeaderVersion.VCF4_2); // if we don't support version fields then we should fail before we ever get here Assert.assertTrue(true); } }
/** Add header with allele frequency */ private void addAFHeader(VCFHeader header, String prefix, String idInfix, String noteInfix, GnomadPopulation pop) { String popName; if (pop == GnomadPopulation.ALL) popName = "all populations"; else popName = pop + " / " + pop.getLabel() + " population"; VCFInfoHeaderLine line = new VCFInfoHeaderLine(prefix + idInfix + "AF_" + pop, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Frequency observed in ExAC data set in " + popName + noteInfix); header.addMetaDataLine(line); }
/** Add header with hom allele counts */ private void addACHomHeader(VCFHeader header, String prefix, String idInfix, String noteInfix, GnomadPopulation pop) { String popName; if (pop == GnomadPopulation.ALL) popName = "all populations"; else popName = pop + " / " + pop.getLabel() + " population"; VCFInfoHeaderLine line = new VCFInfoHeaderLine(prefix + idInfix + "HOM_" + pop, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Overall number of observed homozygous alleles in " + popName + noteInfix); header.addMetaDataLine(line); }
/** Add header with allele counts */ private void addACHeader(VCFHeader header, String prefix, String idInfix, String noteInfix, ThousandGenomesPopulation pop) { String popName; if (pop == ThousandGenomesPopulation.ALL) popName = "all populations"; else popName = pop + " / " + pop.getLabel() + " population"; VCFInfoHeaderLine line = new VCFInfoHeaderLine(prefix + idInfix + "AC_" + pop, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Overall number of observed alleles in " + popName + noteInfix); header.addMetaDataLine(line); }
/** Add header with allele counts */ private void addACHeader(VCFHeader header, String prefix, String idInfix, String noteInfix, GnomadPopulation pop) { String popName; if (pop == GnomadPopulation.ALL) popName = "all populations"; else popName = pop + " / " + pop.getLabel() + " population"; VCFInfoHeaderLine line = new VCFInfoHeaderLine(prefix + idInfix + "AC_" + pop, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Overall number of observed alleles in " + popName + noteInfix); header.addMetaDataLine(line); }
/** Add header with hemi allele counts */ private void addACHemiHeader(VCFHeader header, String prefix, String idInfix, String noteInfix, ThousandGenomesPopulation pop) { String popName; if (pop == ThousandGenomesPopulation.ALL) popName = "all populations"; else popName = pop + " / " + pop.getLabel() + " population"; VCFInfoHeaderLine line = new VCFInfoHeaderLine(prefix + idInfix + "Hemi_" + pop, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Overall number of observed hemizygous alleles in " + popName + noteInfix); header.addMetaDataLine(line); }
/** Add header with allele frequency */ private void addAFHeader(VCFHeader header, String prefix, String idInfix, String noteInfix, ThousandGenomesPopulation pop) { String popName; if (pop == ThousandGenomesPopulation.ALL) popName = "all populations"; else popName = pop + " / " + pop.getLabel() + " population"; VCFInfoHeaderLine line = new VCFInfoHeaderLine(prefix + idInfix + "AF_" + pop, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Frequency observed in thousand genomes data set in " + popName + noteInfix); header.addMetaDataLine(line); }
/** Add header with het allele counts */ private void addACHetHeader(VCFHeader header, String prefix, String idInfix, String noteInfix, ThousandGenomesPopulation pop) { String popName; if (pop != ThousandGenomesPopulation.ALL) popName = "all populations"; else popName = pop + " / " + pop.getLabel() + " population"; VCFInfoHeaderLine line = new VCFInfoHeaderLine(prefix + idInfix + "Het_" + pop, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Overall number of observed heterozygous alleles in " + popName + noteInfix); header.addMetaDataLine(line); }
/** Add header with allele frequency */ private void addAFHeader(VCFHeader header, String prefix, String idInfix, String noteInfix, ExacPopulation pop) { String popName; if (pop == ExacPopulation.ALL) popName = "all populations"; else popName = pop + " / " + pop.getLabel() + " population"; VCFInfoHeaderLine line = new VCFInfoHeaderLine(prefix + idInfix + "AF_" + pop, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Frequency observed in ExAC data set in " + popName + noteInfix); header.addMetaDataLine(line); }
/** Add header with het allele counts */ private void addACHetHeader(VCFHeader header, String prefix, String idInfix, String noteInfix, ExacPopulation pop) { String popName; if (pop != ExacPopulation.ALL) popName = "all populations"; else popName = pop + " / " + pop.getLabel() + " population"; VCFInfoHeaderLine line = new VCFInfoHeaderLine(prefix + idInfix + "HET_" + pop, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Overall number of observed heterozygous alleles in " + popName + noteInfix); header.addMetaDataLine(line); }
/** Add header with hom allele counts */ private void addACHomHeader(VCFHeader header, String prefix, String idInfix, String noteInfix, ExacPopulation pop) { String popName; if (pop == ExacPopulation.ALL) popName = "all populations"; else popName = pop + " / " + pop.getLabel() + " population"; VCFInfoHeaderLine line = new VCFInfoHeaderLine(prefix + idInfix + "HOM_" + pop, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Overall number of observed homozygous alleles in " + popName + noteInfix); header.addMetaDataLine(line); }
public void extendHeader(VCFHeader vcfHeader, String prefix) { VCFInfoHeaderLine inheritanceLine = new VCFInfoHeaderLine(key(prefix), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Compatible inheritance modes (AD, AR, XD, XR, MT)"); vcfHeader.addMetaDataLine(inheritanceLine); VCFInfoHeaderLine subInheritanceLine = new VCFInfoHeaderLine(keySub(prefix), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Extra annotation for recessive inheritance sub type (AR_HOM_ALT, AR_COMP_HET, XR_HOM_ALT, XR_COMP_HET)"); vcfHeader.addMetaDataLine(subInheritanceLine); }
private final static void addHeaderLine(final Set<VCFHeaderLine> metaData, final String id, final VCFHeaderLineCount count, final VCFHeaderLineType type) { metaData.add(new VCFInfoHeaderLine(id, count, type, "x")); if ( type != VCFHeaderLineType.Flag ) metaData.add(new VCFFormatHeaderLine(id, count, type, "x")); }
private final static void addHeaderLine(final Set<VCFHeaderLine> metaData, final String id, final int count, final VCFHeaderLineType type) { metaData.add(new VCFInfoHeaderLine(id, count, type, "x")); if ( type != VCFHeaderLineType.Flag ) metaData.add(new VCFFormatHeaderLine(id, count, type, "x")); }
private static VCFHeader createTestHeader() { final VCFHeader header = new VCFHeader(); header.addMetaDataLine(new VCFInfoHeaderLine(RANDOM_ATTRIBUTE, 1, VCFHeaderLineType.Character, "random string")); return header; }