public String toString() { return toStringEncoding(); }
public String toString() { return toStringEncoding(); }
public String toString() { return toStringEncoding(); }
@Override protected String toStringEncoding() { Map<String, Object> map = new LinkedHashMap<String, Object>(); map.put("ID", name); map.putAll(genericFields); return getKey() + "=" + VCFHeaderLine.toStringEncoding(map); }
protected String toStringEncoding() { Map<String, Object> map = new LinkedHashMap<String, Object>(); map.put("ID", name); map.putAll(genericFields); return getKey() + "=" + VCFHeaderLine.toStringEncoding(map); }
@Override protected String toStringEncoding() { Map<String, Object> map = new LinkedHashMap<String, Object>(); map.put("ID", name); map.putAll(genericFields); return getKey() + "=" + VCFHeaderLine.toStringEncoding(map); }
/** * make a string representation of this header line * @return a string representation */ protected String toStringEncoding() { Map<String,Object> map = new LinkedHashMap<String,Object>(); map.put("ID", name); Object number; switch ( countType ) { case A: number = VCFConstants.PER_ALLELE_COUNT; break; case G: number = VCFConstants.PER_GENOTYPE_COUNT; break; case UNBOUNDED: number = VCFConstants.UNBOUNDED_ENCODING_v4; break; case INTEGER: default: number = count; } map.put("Number", number); map.put("Type", type); map.put("Description", description); return lineType.toString() + "=" + VCFHeaderLine.toStringEncoding(map); }
map.put("Type", type); map.put("Description", description); return lineType.toString() + "=" + VCFHeaderLine.toStringEncoding(map);
map.put("Version", version); return lineType.toString() + "=" + VCFHeaderLine.toStringEncoding(map);
@Test public void testEncodeVCFHeaderLineWithUnescapedQuotes() { final Map<String, String> attributes = new LinkedHashMap<>(); attributes.put("ID", "VariantFiltration"); attributes.put("CommandLineOptions", "filterName=[ANNOTATION] filterExpression=[ANNOTATION == \"NA\" || ANNOTATION <= 2.0]"); final String encodedAttributes = VCFHeaderLine.toStringEncoding(attributes); assertNotNull(encodedAttributes); final String expectedEncoding = "<ID=VariantFiltration,CommandLineOptions=\"filterName=[ANNOTATION] filterExpression=[ANNOTATION == \\\"NA\\\" || ANNOTATION <= 2.0]\">"; assertEquals(encodedAttributes, expectedEncoding); }
@Test public void testEncodeVCFHeaderLineWithEscapedQuotes() { final Map<String, String> attributes = new LinkedHashMap<>(); attributes.put("ID", "VariantFiltration"); attributes.put("CommandLineOptions", "filterName=[ANNOTATION] filterExpression=[ANNOTATION == \\\"NA\\\" || ANNOTATION <= 2.0]"); final String encodedAttributes = VCFHeaderLine.toStringEncoding(attributes); assertNotNull(encodedAttributes); final String expectedEncoding = "<ID=VariantFiltration,CommandLineOptions=\"filterName=[ANNOTATION] filterExpression=[ANNOTATION == \\\"NA\\\" || ANNOTATION <= 2.0]\">"; assertEquals(encodedAttributes, expectedEncoding); }
long chrSize = entry.getValue(); newLines.add(new VCFContigHeaderLine(VCFHeaderLine.toStringEncoding( createContigEntry(currName, chrSize, ARGS.targetAssembly, ARGS.species)), version, VCFConstants.CONTIG_HEADER_KEY, i++));
Assert.assertEquals(firstCopyNewHeaderLine.toStringEncoding(), "GATKCommandLine.Test=<ID=VariantFiltration,CommandLineOptions=\"filterName=[ANNOTATION] filterExpression=[ANNOTATION == \\\"NA\\\" || ANNOTATION <= 2.0]\">"); Assert.assertEquals(secondCopyNewHeaderLine.toStringEncoding(), "GATKCommandLine.Test=<ID=VariantFiltration,CommandLineOptions=\"filterName=[ANNOTATION] filterExpression=[ANNOTATION == \\\"NA\\\" || ANNOTATION <= 2.0]\">");