/**
* Add up overlap btw the blocks in this chain and the given interval.
*
* @return Length of overlap, offsets into first and last ContinuousBlocks, and indices of first
* and last ContinuousBlocks.
*/
private static TargetIntersection targetIntersection(final Chain chain, final Interval interval) {
int intersectionLength = 0;
// Convert interval to 0-based, half-open
int start = interval.getStart() - 1;
int end = interval.getEnd();
int firstBlockIndex = -1;
int lastBlockIndex = -1;
int startOffset = -1;
int offsetFromEnd = -1;
List<Chain.ContinuousBlock> blockList = chain.getBlocks();
for (int i = 0; i < blockList.size(); ++i) {
final Chain.ContinuousBlock block = blockList.get(i);
if (block.fromStart >= end) {
break;
} else if (block.getFromEnd() <= start) {
continue;
}
if (firstBlockIndex == -1) {
firstBlockIndex = i;
if (start > block.fromStart) {
startOffset = start - block.fromStart;
} else {
startOffset = 0;
}
}
lastBlockIndex = i;
if (block.getFromEnd() > end) {
offsetFromEnd = block.getFromEnd() - end;
} else {
offsetFromEnd = 0;
}
int thisIntersection = Math.min(end, block.getFromEnd()) - Math.max(start, block.fromStart);
if (thisIntersection <= 0) {
throw new PicardException("Should have been some intersection.");
}
intersectionLength += thisIntersection;
}
if (intersectionLength == 0) {
return null;
}
return new TargetIntersection(
chain, intersectionLength, startOffset, offsetFromEnd, firstBlockIndex, lastBlockIndex);
}
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 String toString() {
if (toInterval == null) {
// Matched a chain, but entirely within a gap.
return fromInterval.toString()
+ " (len "
+ fromInterval.length()
+ ")=>null using chain "
+ chainId;
}
final String strand = toInterval.isNegativeStrand() ? "-" : "+";
return fromInterval.toString()
+ " (len "
+ fromInterval.length()
+ ")=>"
+ toInterval
+ "("
+ strand
+ ") using chain "
+ chainId
+ " ; pct matched "
+ percentLiftedOver;
}
/**
* 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);
}