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#!/usr/bin/env perl

...

    return;
}

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$ cat pm_1084445_locations.txt
chromosome1 100 100 . G T several other columns
...
chromosome3 110 110 . A C several other columns
chromosome3 200 200 . C T several other columns
chromosome4 125 125 . C T several other columns

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$ pm_1084445_locations.pl
chromosome1 100 100 . G T several other columns
chromosome2 125 125 . C T several other columns
chromosome3 100 100 . G T several other columns
chromosome4 125 125 . C T several other columns

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$ pm_1084445_locations.pl
chromosome1 110 110 . A C several other columns
chromosome1 200 200 . C T several other columns
chromosome2 125 125 . C T several other columns
chromosome3 100 100 . G T several other columns

Select or download this

$ pm_1084445_locations.pl
chromosome1 100 100 . G T several other columns
chromosome2 125 125 . C T several other columns
chromosome3 110 110 . A C several other columns
chromosome3 200 200 . C T several other columns