public VariantBuilder setCiEnd(int left, int right) { initSv(); sv.setCiEndLeft(left); sv.setCiEndRight(right); return this; }
public VariantBuilder setSvInsSeq(String left, String right) { initSv(); sv.setLeftSvInsSeq(left); sv.setRightSvInsSeq(right); return this; }
public VariantBuilder setCiStart(int left, int right) { initSv(); sv.setCiStartLeft(left); sv.setCiStartRight(right); return this; }
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)); } }
private void parseStart(String start, String variantString) { if (StringUtils.contains(start, '<')) { String[] split = start.split("<", -1); if (split.length != 3) { throw new IllegalArgumentException("Error parsing start from variant " + variantString + ". Expected 3 fields separated by '<'. " + "Format: \"" + VARIANT_STRING_FORMAT + "\""); } initSv(); if (!split[0].isEmpty()) { sv.setCiStartLeft(Integer.parseInt(split[0])); } setStart(Integer.parseInt(split[1])); if (!split[2].isEmpty()) { sv.setCiStartRight(Integer.parseInt(split[2])); } } else { setStart(Integer.parseInt(start)); } }
private void parseAlternate(String alternate) { int idx = alternate.indexOf("..."); if (idx >= 0) { setAlternate(INS_ALT); initSv(); sv.setLeftSvInsSeq(alternate.substring(0, idx)); sv.setRightSvInsSeq(alternate.substring(idx + 3)); } else { setAlternate(alternate); } }
public VariantBuilder setCopyNumber(int copyNumber) { initSv(); sv.setCopyNumber(copyNumber); sv.setType(getCNVSubtype(copyNumber)); return this; }
public void inferSV() { if (isSV(type)) { initSv(); switch (type) {