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; }
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(), interval.isNegativeStrand(), targetIntersection); float percentLiftedOver = targetIntersection.intersectionLength/(float)interval.length(); ret.add(new PartialLiftover(intersectingChain, toInterval, targetIntersection.chain.id, percentLiftedOver)); } } return ret; }
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(), interval.isNegativeStrand(), targetIntersection); float percentLiftedOver = targetIntersection.intersectionLength/(float)interval.length(); ret.add(new PartialLiftover(intersectingChain, toInterval, targetIntersection.chain.id, percentLiftedOver)); } } return ret; }
final TargetIntersection candidateIntersection = targetIntersection(chain, interval); if (candidateIntersection != null && candidateIntersection.intersectionLength >= minMatchSize) { if (chainHit != null) {
final TargetIntersection candidateIntersection = targetIntersection(chain, interval); if (candidateIntersection != null && candidateIntersection.intersectionLength >= minMatchSize) { if (chainHit != null) {
final TargetIntersection candidateIntersection = targetIntersection(chain, interval); if (candidateIntersection != null && candidateIntersection.intersectionLength >= minMatchSize) { if (chainHit != null) {