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chr10
chr10_random
...
chrX
chrX_random
chrY

chr1    100    159    0
chr1    200    260    0
...
chr11    679    687    0
chr22    100    200    0
chr22    300    400    0

#!/usr/bin/perl
use warnings; use strict;
...
}
close(KEY);
close(REG);

chr1    100    159    0
chr1    200    260    0
chr1    500    750    0

chr3    450    700    0

chr4    100    300    0

chr7    350    600    0

chr9    100    125    0

chr11    679    687    0

chr22    100    200    0
chr22    300    400    0