/**
* Throw an exception if all the "to" sequence names in the chains are not found in the given
* sequence dictionary.
*/
public void validateToSequences(final SAMSequenceDictionary sequenceDictionary) {
for (final Chain chain : chains.getAll()) {
if (sequenceDictionary.getSequence(chain.toSequenceName) == null) {
throw new PicardException(
"Sequence "
+ chain.toSequenceName
+ " from chain file is not found in sequence dictionary.");
}
}
}
/**
* Lift over the given interval to the new genome build.
*
* @param interval Interval to be lifted over.
* @param liftOverMinMatch Minimum fraction of bases that must remap.
* @return Interval in the output build coordinates, or null if it cannot be lifted over.
*/
public Interval liftOver(final Interval interval, final double liftOverMinMatch) {
if (interval.length() == 0) {
throw new IllegalArgumentException(
"Zero-length interval cannot be lifted over. Interval: " + interval.getName());
}
Chain chainHit = null;
TargetIntersection targetIntersection = null;
// Number of bases in interval that can be lifted over must be >= this.
double minMatchSize = liftOverMinMatch * interval.length();
// Find the appropriate Chain, and the part of the chain corresponding to the interval to be
// lifted over.
for (final Chain chain : chains.getOverlaps(interval)) {
final TargetIntersection candidateIntersection = targetIntersection(chain, interval);
if (candidateIntersection != null
&& candidateIntersection.intersectionLength >= minMatchSize) {
if (chainHit != null) {
// In basic liftOver, multiple hits are not allowed.
return null;
}
chainHit = chain;
targetIntersection = candidateIntersection;
} else if (candidateIntersection != null) {
LOG.info(
"Interval "
+ interval.getName()
+ " failed to match chain "
+ chain.id
+ " because intersection length "
+ candidateIntersection.intersectionLength
+ " < minMatchSize "
+ minMatchSize
+ " ("
+ (candidateIntersection.intersectionLength / (float) interval.length())
+ " < "
+ liftOverMinMatch
+ ")");
}
}
if (chainHit == null) {
// Can't be lifted over.
return null;
}
return createToInterval(interval.getName(), targetIntersection);
}
public List<PartialLiftover> diagnosticLiftover(final Interval interval) {
final List<PartialLiftover> ret = new ArrayList<PartialLiftover>();
if (interval.length() == 0) {
throw new IllegalArgumentException(
"Zero-length interval cannot be lifted over. Interval: " + interval.getName());
}
for (final Chain chain : chains.getOverlaps(interval)) {
Interval intersectingChain = interval.intersect(chain.interval);
final TargetIntersection targetIntersection = targetIntersection(chain, intersectingChain);
if (targetIntersection == null) {
ret.add(new PartialLiftover(intersectingChain, chain.id));
} else {
Interval toInterval = createToInterval(interval.getName(), targetIntersection);
float percentLiftedOver = targetIntersection.intersectionLength / (float) interval.length();
ret.add(
new PartialLiftover(
intersectingChain, toInterval, targetIntersection.chain.id, percentLiftedOver));
}
}
return ret;
}