public SAMReadGroupRecord(final String id, final SAMReadGroupRecord srcProgramRecord) { mReadGroupId = id; for (final Map.Entry<String, String> entry : srcProgramRecord.getAttributes()) { setAttribute(entry.getKey(), entry.getValue()); } }
public SAMReadGroupRecord(final String id, final SAMReadGroupRecord srcProgramRecord) { mReadGroupId = id; for (final Map.Entry<String, String> entry : srcProgramRecord.getAttributes()) { setAttribute(entry.getKey(), entry.getValue()); } }
public SAMReadGroupRecord(final String id, final SAMReadGroupRecord srcProgramRecord) { mReadGroupId = id; for (final Map.Entry<String, String> entry : srcProgramRecord.getAttributes()) { setAttribute(entry.getKey(), entry.getValue()); } }
protected String getRGLine(final SAMReadGroupRecord readGroup) { final String[] fields = new String[2 + readGroup.getAttributes().size()]; fields[0] = HEADER_LINE_START + HeaderRecordType.RG; fields[1] = SAMReadGroupRecord.READ_GROUP_ID_TAG + TAG_KEY_VALUE_SEPARATOR + readGroup.getReadGroupId(); encodeTags(readGroup, fields, 2); return StringUtil.join(FIELD_SEPARATOR, fields); }
protected String getRGLine(final SAMReadGroupRecord readGroup) { final String[] fields = new String[2 + readGroup.getAttributes().size()]; fields[0] = HEADER_LINE_START + HeaderRecordType.RG; fields[1] = SAMReadGroupRecord.READ_GROUP_ID_TAG + TAG_KEY_VALUE_SEPARATOR + readGroup.getReadGroupId(); encodeTags(readGroup, fields, 2); return StringUtil.join(FIELD_SEPARATOR, fields); }
for (final Map.Entry<String, String> attributeEntry : rgRecord.getAttributes()) { sortedAttributes.put(attributeEntry.getKey(), attributeEntry.getValue());
for (final Map.Entry<String, String> attributeEntry : rgRecord.getAttributes()) { sortedAttributes.put(attributeEntry.getKey(), attributeEntry.getValue());
for (final Map.Entry<String, String> attributeEntry : rgRecord.getAttributes()) { sortedAttributes.put(attributeEntry.getKey(), attributeEntry.getValue());
for (final Map.Entry<String, String> attributeEntry : rgRecord.getAttributes()) { sortedAttributes.put(attributeEntry.getKey(), attributeEntry.getValue());
private void writeRGLine(final SAMReadGroupRecord readGroup) { final String[] fields = new String[2 + readGroup.getAttributes().size()]; fields[0] = HEADER_LINE_START + HeaderRecordType.RG; fields[1] = SAMReadGroupRecord.READ_GROUP_ID_TAG + TAG_KEY_VALUE_SEPARATOR + readGroup.getReadGroupId(); encodeTags(readGroup, fields, 2); println(StringUtil.join(FIELD_SEPARATOR, fields)); }
for (Map.Entry<String,String> entry :rg.getAttributes()){ attr.put(entry.getKey(), entry.getValue());