public static Pair<Boolean, CigarElement> readStartsWithInsertion(final Cigar cigar) {
for (CigarElement cigarElement : cigar.getCigarElements()) {
if (cigarElement.getOperator() == CigarOperator.INSERTION)
return new Pair<Boolean, CigarElement>(true, cigarElement);
else if (cigarElement.getOperator() != CigarOperator.HARD_CLIP
&& cigarElement.getOperator() != CigarOperator.SOFT_CLIP) break;
}
return new Pair<Boolean, CigarElement>(false, null);
}
public static Pair<Integer, Boolean> getReadCoordinateForReferenceCoordinate(
final int alignmentStart,
final Cigar cigar,
final int refCoord,
final boolean allowGoalNotReached) {
int readBases = 0;
int refBases = 0;
boolean fallsInsideDeletion = false;
int goal = refCoord - alignmentStart; // The goal is to move this many reference bases
if (goal < 0) {
if (allowGoalNotReached) {
return new Pair<Integer, Boolean>(CLIPPING_GOAL_NOT_REACHED, false);
} else {
throw new ReviewedStingException(
"Somehow the requested coordinate is not covered by the read. Too many deletions?");
}
}
boolean goalReached = refBases == goal;
Iterator<CigarElement> cigarElementIterator = cigar.getCigarElements().iterator();
while (!goalReached && cigarElementIterator.hasNext()) {
CigarElement cigarElement = cigarElementIterator.next();
int shift = 0;
if (cigarElement.getOperator().consumesReferenceBases()
|| cigarElement.getOperator() == CigarOperator.SOFT_CLIP) {
if (refBases + cigarElement.getLength() < goal) shift = cigarElement.getLength();
else shift = goal - refBases;
refBases += shift;
}
goalReached = refBases == goal;
if (!goalReached && cigarElement.getOperator().consumesReadBases())
readBases += cigarElement.getLength();
if (goalReached) {
// Is this base's reference position within this cigar element? Or did we use it all?
boolean endsWithinCigar = shift < cigarElement.getLength();
// If it isn't, we need to check the next one. There should *ALWAYS* be a next one
// since we checked if the goal coordinate is within the read length, so this is just a
// sanity check.
if (!endsWithinCigar && !cigarElementIterator.hasNext()) {
if (allowGoalNotReached) {
return new Pair<Integer, Boolean>(CLIPPING_GOAL_NOT_REACHED, false);
} else {
throw new ReviewedStingException(
"Reference coordinate corresponds to a non-existent base in the read. This should never happen -- call Mauricio");
}
}
CigarElement nextCigarElement;
// if we end inside the current cigar element, we just have to check if it is a deletion
if (endsWithinCigar)
fallsInsideDeletion = cigarElement.getOperator() == CigarOperator.DELETION;
// if we end outside the current cigar element, we need to check if the next element is an
// insertion or deletion.
else {
nextCigarElement = cigarElementIterator.next();
// if it's an insertion, we need to clip the whole insertion before looking at the next
// element
if (nextCigarElement.getOperator() == CigarOperator.INSERTION) {
readBases += nextCigarElement.getLength();
if (!cigarElementIterator.hasNext()) {
if (allowGoalNotReached) {
return new Pair<Integer, Boolean>(CLIPPING_GOAL_NOT_REACHED, false);
} else {
throw new ReviewedStingException(
"Reference coordinate corresponds to a non-existent base in the read. This should never happen -- call Mauricio");
}
}
nextCigarElement = cigarElementIterator.next();
}
// if it's a deletion, we will pass the information on to be handled downstream.
fallsInsideDeletion = nextCigarElement.getOperator() == CigarOperator.DELETION;
}
// If we reached our goal outside a deletion, add the shift
if (!fallsInsideDeletion && cigarElement.getOperator().consumesReadBases())
readBases += shift;
// If we reached our goal inside a deletion, but the deletion is the next cigar element then
// we need
// to add the shift of the current cigar element but go back to it's last element to return
// the last
// base before the deletion (see warning in function contracts)
else if (fallsInsideDeletion && !endsWithinCigar) readBases += shift - 1;
// If we reached our goal inside a deletion then we must backtrack to the last base before
// the deletion
else if (fallsInsideDeletion && endsWithinCigar) readBases--;
}
}
if (!goalReached) {
if (allowGoalNotReached) {
return new Pair<Integer, Boolean>(CLIPPING_GOAL_NOT_REACHED, false);
} else {
throw new ReviewedStingException(
"Somehow the requested coordinate is not covered by the read. Alignment "
+ alignmentStart
+ " | "
+ cigar);
}
}
return new Pair<Integer, Boolean>(readBases, fallsInsideDeletion);
}