Your solution is an excellent use of a HoH! Here are a few items to consider within your foreach:

foreach (@ARGV) {
    open my $fh, '<', $_ or die $!;
    while ( my $line = <$fh> ) {
        next unless my @p = $line =~ /^(chr.+?)\t+(\d+)\t+(\d+)/;

        $minmax{ $p[0] }{min} //= $p[1];
        $minmax{ $p[0] }{max} //= $p[2];

        if ( $p[1] < $minmax{ $p[0] }{min} ) {
            $minmax{ $p[0] }{min} = $p[1];
        }

        if ( $p[2] > $minmax{ $p[0] }{max} ) {
            $minmax{ $p[0] }{max} = $p[2];
        }
    }
    close $fh;
}
[download]

• A three-argument open is used
• A lexically-scoped variable is used for the file handle
• or die $! checks for open errors
• The regex line:
• Skips possible comment and track definition lines in the BED files
• And then makes using chomp and split unnecessary
• Uses defined-or-equals (//=) to replace the !exists

Hope this is helpful.

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