public VariantBuilder setFilter(String filter) { addAttribute(StudyEntry.FILTER, filter); return this; }
public VariantBuilder setQuality(String quality) { addAttribute(StudyEntry.QUAL, quality); return this; }
public VariantBuilder setQuality(Double quality) { if (quality == null || quality == VariantContext.NO_LOG10_PERROR) { addAttribute(StudyEntry.QUAL, "."); } else { addAttribute(StudyEntry.QUAL, quality.toString()); } return this; }
public VariantBuilder addAttribute(String key, List<?> values) { return addAttribute(key, StringUtils.join(values, VCFConstants.INFO_FIELD_ARRAY_SEPARATOR)); }
public VariantBuilder addAttribute(String key, Number value) { return addAttribute(key, value.toString()); }
builder.addAttribute(key, variantContext.getAttributeAsList(key)); } else { builder.addAttribute(key, variantContext.getAttributeAsString(key, ""));
.setFilter("PASS_" + fileId) .setQuality(fileId * 100.0) .addAttribute("AD", ad) .setFormat("GT", "DP", "GQX", "AD");
public static Variant newVariant(String chromosome, int start, int end, String reference, String alternate, Integer fileId, Integer studyId) { int pad = (fileId - 1) * NUM_SAMPLES; return Variant.newBuilder() .setChromosome(chromosome) .setStart(start) .setEnd(end) .setReference(reference) .setAlternate(alternate) .setStudyId(studyId.toString()) .setFileId(fileId.toString()) .setFilter("PASS_" + fileId) .setQuality(fileId * 100.0) .addAttribute("AD", "1,2") .setFormat("GT", "DP", "GQX", "AD") .addSample("S" + (1 + pad), "./.", String.valueOf(11 + pad), "0.7", "1,2") .addSample("S" + (2 + pad), "1/1", String.valueOf(12 + pad), "0.7", "1,2") .addSample("S" + (3 + pad), "0/0", String.valueOf(13 + pad), "0.7", "1,2") .addSample("S" + (4 + pad), "1/0", String.valueOf(14 + pad), "0.7", "1,2").build(); }
.setFilter("PASS") .setQuality(200.0) .addAttribute("k1", "v1") .build(); .setFilter("PASS:Low") .setQuality(210.0) .addAttribute("k2", "v2") .addAttribute("k22", "v22") .build();