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#awk -f cutLa.awk extra_cuts.txt test.la

(NR==FNR){

	++c[$1]

	sites[$1,c[$1]]=$2

}

(NR!=FNR){

	if ($1 in c) {

		start = $7+0

		end = $8+0

		orientation=$4

		found = 0

		for (i = 1; i <= c[$1]; ++i) {

			s = sites[$1, i]

			if (s > start && s < end) {

				print $1"\t"start"\t"s"\t"orientation

				start = s + 1

				++found

			}

		}

		if (found > 0)

			print $1"\t"start"\t"end"\t"orientation

		else

			print

	} else

		print

}