while (<$IN2>) {
    chomp $_;
    next if eof;
    my @F2      = split( "\t", $_ );          #Split each tab-delimited field
    my $partner = <$IN2>;
    my @F3      = split( "\t", $partner );    #Split each tab-delimited field
    $store{ ( abs( $F2[2] - $F3[2] ) + 1 ) }++;
    ( $F2[2], $F3[2] ) = ( $F3[2], $F2[2] ) if $F2[2] > $F3[2];
    $Tally{ $F2[1] }{ $F2[2] }{ $F3[2] }++;
}
foreach my $key ( sort { $a <=> $b } keys %store ) {
    print $OUT4 "$key\t$store{$key}\n";
}
foreach my $chr ( sort { $a <=> $b } keys %Tally ) {
    foreach my $value1 ( sort { $a <=> $b } keys %{ $Tally{$chr} } ) {
        foreach
          my $value2 ( sort { $a <=> $b } keys %{ $Tally{$chr}{$value1} } )
        {
            print $OUT5
              "$chr\t$value1\t$value2\t$Tally{$chr}{$value1}{$value2}\n";
        }
    }
}

##</code><code>##

Use of uninitialized value in subtraction (-) at line 117, <$IN2> line 4148567.
Use of uninitialized value in numeric gt (>) at line 118, <$IN2> line 4148567.
Use of uninitialized value $F2[2] in hash element at line 119, <$IN2> line 4148567.
Argument "" isn't numeric in sort at line 127, <$IN2> line 4148567.

##</code><code>##

Line 117 - $store{(abs($F2[2]-$F3[2])+1)}++;
Line 118 - ($F2[2], $F3[2]) = ($F3[2], $F2[2]) if $F2[2] > $F3[2];
Line 119 - $Tally{$F2[1]}{$F2[2]}{$F3[2]}++;
Line 127 - foreach my $value1 (sort {$a <=> $b} keys %{$Tally{$chr}}) {

##</code><code>##

w	11	99658	75	75M	0
c	11	99999	75	75M	74
w	2	702424	75	75M	0
c	2	702556	75	75M	74
c	13	82486	75	75M	74
w	13	82171	75	75M	0
c	2	702585	75	75M	74
w	2	702390	75	75M	0
c	18	2529	75	75M	74
w	18	2232	75	75M	0
c	12	264648	75	75M	74
w	12	264366	74	74M	0
c	10	177758	75	75M	74
w	10	177438	74	74M	0
w	7	185488	74	74M	0