Hello Perl Monks! I am having difficulty discerning the source of an error in my code and or/input data. I attempt to filter data from one file to another based on what I call start and end positions. 

 open (CG, "<$cg_input") or die "can't open $cg_input\n";
my @SNPs = <CG>;
close(CG); 

my $interval = "/Users/logancurtis-whitchurch/Desktop/chrX_divisions/"
+."$region"."_$filter".".txt"; #specifiecs intervals by region and fil
+ter version
open (INTERVAL, "<$interval") or die "can't open interval file\n";
foreach ( <INTERVAL> ) {
    
    my (undef, $start, $end) = split '\s+', $_;
    
    my $switch = 1; 
    while ($switch == 1) {         
    
        my @get_SNPs = split('\s+', $SNPs[$placeholder]);
        my $position = $get_SNPs[3];
                
        if (($position < $start) && ($position < $end)) {
            $placeholder++;
        }
        
        if (($position >= $start) && ($position <= $end)) {
            print OUT "@get_SNPs\n";
            $placeholder++;
        }
        if (($position > $start) && ($position > $end)) {
            $switch =! 1;    
        }
    }
}
close(INTERVAL);

[download]

The error message returned to me is as follows on repeating loop, until I terminate the program. Line 246 of my interval input file corresponds to the last line of the file, which looks no different from any of the others. I am at a loss regarding the uninitialized value, especially when identically formatted files have worked with the same code.

 Use of uninitialized value in split at filter.CGS.pl line 43, <INTERV
+AL> line 264.
Use of uninitialized value $position in numeric lt (<) at filter.CGS.p
+l line 46, <INTERVAL> line 264.
Use of uninitialized value $position in numeric lt (<) at filter.CGS.p
+l line 46, <INTERVAL> line 264.
Use of uninitialized value $position in numeric ge (>=) at filter.CGS.
+pl line 50, <INTERVAL> line 264.
Use of uninitialized value $position in numeric gt (>) at filter.CGS.p
+l line 54, <INTERVAL> line 264.
Use of uninitialized value in split at filter.CGS.pl line 43, <INTERVA
+L> line 264.

[download]

In reply to Tracing an Uninitialized Error by ccelt09

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