private void parseEnd(String end, String variantString) { if (StringUtils.contains(end, '<')) { String[] split = end.split("<", -1); if (split.length != 3) { throw new IllegalArgumentException("Error parsing end from variant " + variantString + ". Expected 3 fields separated by '<'. " + "Format: \"" + VARIANT_STRING_FORMAT + "\""); } initSv(); if (!split[0].isEmpty()) { sv.setCiEndLeft(Integer.parseInt(split[0])); } setEnd(Integer.parseInt(split[1])); if (!split[2].isEmpty()) { sv.setCiEndRight(Integer.parseInt(split[2])); } } else { setEnd(Integer.parseInt(end)); } }
.setChromosome(variantContext.getContig()) .setStart(variantContext.getStart()) .setEnd(variantContext.getEnd()) .setStudyId(studyId) .setFileId(fileId);
.setChromosome(chromosome) .setStart(start) .setEnd(end) .setReference(reference) .setAlternates(alternates)
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(); }