/**
* Calculates the reference coordinate for a read coordinate
*
* @param read the read
* @param offset the base in the read (coordinate in the read)
* @return the reference coordinate correspondent to this base
*/
public static long getReferenceCoordinateForReadCoordinate(GATKSAMRecord read, int offset) {
if (offset > read.getReadLength())
throw new ReviewedStingException(
String.format(OFFSET_OUT_OF_BOUNDS_EXCEPTION, offset, read.getReadLength()));
long location = read.getAlignmentStart();
Iterator<CigarElement> cigarElementIterator = read.getCigar().getCigarElements().iterator();
while (offset > 0 && cigarElementIterator.hasNext()) {
CigarElement cigarElement = cigarElementIterator.next();
long move = 0;
if (cigarElement.getOperator().consumesReferenceBases())
move = (long) Math.min(cigarElement.getLength(), offset);
location += move;
offset -= move;
}
if (offset > 0 && !cigarElementIterator.hasNext())
throw new ReviewedStingException(OFFSET_NOT_ZERO_EXCEPTION);
return location;
}
/**
* Is a base inside a read?
*
* @param read the read to evaluate
* @param referenceCoordinate the reference coordinate of the base to test
* @return true if it is inside the read, false otherwise.
*/
public static boolean isInsideRead(final GATKSAMRecord read, final int referenceCoordinate) {
return referenceCoordinate >= read.getAlignmentStart()
&& referenceCoordinate <= read.getAlignmentEnd();
}