is there a way to restrict the behaviour of bedtools to a line-by-line comparison?
To be more clear, if I have 2 BED files:
chr1 1 100 chr2 1 100
chr2 50 70 chr3 1 100
I'd like bedtools subtract to eliminate from File_A the interval contained in one line only if the interval in the corresponding line in file_B overlap. Therefore, in the present example no intervals should be subtracted from File_A, but I think by default bedtools is scanning one interval of File_A against all other intervals of File_B.
Is this possible?
Thank you in advance!