The problem is that your $placeholder value isn't set back to 0 when you finish testing a range, so you never go back to test the previous lines. The solution to your problem would be to add a $placeholder = 0 at the end of your foreach loop.

Now, if you want some advice on your code, first, I would have gone the other way around, have all the ranges in memory, and for each line of your data, test all ranges. And to keep track of the file that needs to be written on, an array of hashes could do the trick. Something like :

[
   { start => 1, end => 1001, file => *FH1 },
   { start => 500, end => 2001, file => *FH2 }
]
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for each line
   $position = getPosition()
   for $range in @ranges
      print $range->{FH} $line if (($position > $range->{start}) && ($
+position < $range->{end}))
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Then, maybe you don't want to rewrite your whole code (that's why I didn't bother much), still, there are some useful things you might like to know. If you want to have a "do something for each value and stop when condition" construct in Perl, you can use the last keyword inside a foreach loop. In your case that would be :

SNP:for my $snp (@SNPs) {
        my @get_SNPs = split(/\t/, $snp);
        my $position = $get_SNPs[3];

        last SNP if ($position > $end); # stop reading, we're out of r
+ange !
                                        
        if (($position >= $start) && ($position <= $end)) {
            print OUT "@get_SNPs";
        }
    }
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Also, instead of

@array = split /\t/, $string;
my $v1 = $array[1];
my $v2 = $array[2];
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