/**
* Returns the mate for a paired-end read. Please note that this method will return an unmapped
* mate for any single end read as well. Do check if the read is paired before calling getMate().
*
* @return The mate, or a constant unmapped mate (for single end reads, or paired end where the
* mate is not found).
*/
public ReadMate getMate() {
if (entry.hasPairAlignmentLink()) {
Alignments.RelatedAlignmentEntry link = entry.getPairAlignmentLink();
String mateChr = getChromosome(link.getTargetIndex());
int mateStart = link.getPosition();
boolean mateNegativeStrand = EntryFlagHelper.isMateReverseStrand(entry);
boolean isReadUnmappedFlag = EntryFlagHelper.isReadUnmapped(entry);
final ReadMate mate =
new ReadMate(mateChr, mateStart, mateNegativeStrand, isReadUnmappedFlag);
return mate;
} else {
return unmappedMate;
}
}
