/**
* 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;
}
}
/**
* Verify that the list has an appropriate unbroken chain of back links.
*
* @param list the list of splices to validate
* @return true if the list has an unbroken chain of back links
*/
boolean spliceListIsValid(final ObjectArrayList<GobyAlignment> list) {
if (list != null && list.size() > 1) {
Alignments.AlignmentEntry prevEntry = list.get(0).entry;
for (int i = 1; i < list.size(); i++) {
Alignments.AlignmentEntry currentEntry = list.get(i).entry;
if (!currentEntry.hasSplicedBackwardAlignmentLink()) return false;
else {
Alignments.RelatedAlignmentEntry currentBackwardLink =
currentEntry.getSplicedBackwardAlignmentLink();
if ((prevEntry.getQueryIndex() != currentEntry.getQueryIndex())
|| (prevEntry.getFragmentIndex() != currentBackwardLink.getFragmentIndex())
|| (prevEntry.getPosition() != currentBackwardLink.getPosition())
|| (prevEntry.getTargetIndex() != currentBackwardLink.getTargetIndex())) {
return false;
}
}
prevEntry = currentEntry;
}
}
return true;
}