/**
* Generates tab delimited string containing details about the passed SAMReadGroupRecord
*
* @param readGroupRecord record
* @return tab delimited string containing details about the SAMReadGroupRecord
*/
private String getReadGroupDetails(final SAMReadGroupRecord readGroupRecord) {
final List<String> elements = new ArrayList<>(5);
final String tmp[] =
readGroupRecord
.getPlatformUnit()
.split("\\."); // Expect to look like: D047KACXX110901.1.ACCAACTG
String runBarcode = "?";
String lane = "?";
String molBarcode = "?";
if ((tmp.length == 3) || (tmp.length == 2)) {
runBarcode = tmp[0];
lane = tmp[1];
molBarcode =
(tmp.length == 3)
? tmp[2]
: ""; // In older BAMS there may be no molecular barcode sequence
} else {
log.error("Unexpected format " + readGroupRecord.getPlatformUnit() + " for PU attribute");
}
elements.add(runBarcode);
elements.add(lane);
elements.add(molBarcode);
elements.add(readGroupRecord.getLibrary());
elements.add(readGroupRecord.getSample());
return String.join("\t", elements);
}
/** Get the ID of the readgroup. */
public static String getID(final SAMReadGroupRecord rg) {
final String pu = rg.getPlatformUnit();
return pu == null ? rg.getId() : pu;
}
/**
* Returns the platform unit associated with the provided read's read group.
*
* @param read read whose platform unit to retrieve
* @param header SAM header containing read groups
* @return the platform unit for the provided read's read group as a String, or null if the read
* has no read group.
*/
public static String getPlatformUnit(final GATKRead read, final SAMFileHeader header) {
final SAMReadGroupRecord readGroup = getSAMReadGroupRecord(read, header);
return readGroup != null ? readGroup.getPlatformUnit() : null;
}