/**
* Creates an "empty" read with the provided read's read group and mate information, but empty
* (not-null) fields: - Cigar String - Read Bases - Base Qualities
*
* <p>Use this method if you want to create a new empty read based on another read
*
* @param read a read to copy fields from
* @return a read with no bases but safe for the GATK
*/
public static GATKRead emptyRead(final GATKRead read) {
final GATKRead emptyRead = read.copy();
emptyRead.setCigar("");
emptyRead.setBases(new byte[0]);
emptyRead.setBaseQualities(new byte[0]);
emptyRead.clearAttributes();
String readGroup = read.getReadGroup();
if (readGroup != null) {
emptyRead.setAttribute(SAMTag.RG.name(), readGroup);
}
return emptyRead;
}
/**
* Returns a {@link SAMReadGroupRecord} object corresponding to the provided read's read group.
*
* @param read read whose read group to retrieve
* @param header SAM header containing read groups
* @return a {@link SAMReadGroupRecord} object corresponding to the provided read's read group, or
* null if the read has no read group
*/
public static SAMReadGroupRecord getSAMReadGroupRecord(
final GATKRead read, final SAMFileHeader header) {
final String readGroupName = read.getReadGroup();
return readGroupName != null ? header.getReadGroup(readGroupName) : null;
}