/**
* Return the number of bps before loc in the sorted set
*
* @param loc the location before which we are counting bases
* @return
*/
public long sizeBeforeLoc(GenomeLoc loc) {
long s = 0;
for (GenomeLoc e : this) {
if (e.isBefore(loc)) s += e.size();
else if (e.isPast(loc)) ; // don't do anything
else // loc is inside of s
s += loc.getStart() - e.getStart();
}
return s;
}
/**
* Return the size, in bp, of the genomic regions by all of the regions in this set
*
* @return size in bp of the covered regions
*/
public long coveredSize() {
long s = 0;
for (GenomeLoc e : this) s += e.size();
return s;
}