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[
    ['NM_144963','2713','4091'],
    ['NM_144963','1949','2712']
];

    my @sorted = sort {($a->[1] <=>$b->[1]) || ($a->[2] <=> $b->[2])}@
+array;
    my $coverage = 0;
...
        $coverage += $_->[2] - $_->[1] +1;
    }
    printf "cover = %.1f%% \n", $coverage/$length *100;

[
    ['NM_176827','618','710'],
...
    ['NM_176827','622','692'],
    ['NM_176827','629','710']
]