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#!/usr/bin/env perl

...
}

close $testfile;

$ cat > pm_least_diff.ref
chr1    40
...
chr2    60
chr2    80
chr3    100

$ cat > pm_least_diff.test
chr1    30
chr2    20
chr2    50
chr3    80

$ pm_least_diff.pl pm_least_diff.ref pm_least_diff.test
chr1    10
chr2    40
chr2    10
chr3    20