#A function that removes breakpoints - After a breakpoint is removed, it attempts to reconstruct the mosaic,
#by finding the two closest segments that can be thought as consecutive. The criterion is

#remove.list - a list of indices of the breakpoints that should be removed
remove.and.reconstruct <- function(remove.list, breakpoints){
	rem.indeces = c()
	for (index in remove.list){
		del.from = del.to = index
		#if it's first or last bp in chromosome ok:
		if ((breakpoints[index,2]==breakpoints[index-1,2]) & (breakpoints[index,2] == breakpoints[index+1,2])){
			current.chunk = breakpoints[which((breakpoints[,1]==breakpoints[index,1]) & (breakpoints[,2]==breakpoints[index,2])),]
			bef = current.chunk[1:index,"left.founder"]
			aft = current.chunk[(index+1):nrow(current.chunk),"left.founder"]
			matching.distances = match(bef, aft) + (length(bef)-1):0
			if (length(na.omit(matching.distances))>0){		
				dist = min(na.omit(matching.distances))
				print(dist)
				del.from = max(which(matching.distances == dist))
				del.to = del.from + dist - 1
			} 
		}
		rem.indeces = c(rem.indeces, del.from:del.to)
	}
	breakpoints = breakpoints[-rem.indeces,]
	print(rem.indeces)
	return(breakpoints)
}