I might suggest the reformatted code.

my %file1;
while(<INPUT1>){
    chomp;
    (my $id, my $number) = split /\t/;
    
    if ($id=~ m/^(CLS_S3_Contig[0-9]+)([-]?)([0-9]+)([_]?)([0-9]+)$/i)
+ {
        $file1{$1} = [$3-8, $5+7]; # or should it be $5+8?
    }
}
print "Processed $. lines from $ARGV[0] file\n";
close(INPUT1);
[download]

This method only saves the low and high ends of the range instead of each number in the range. Then, in your second while loop, you only need to check if $current_line[1] falls in between the low and high ends of the range. Your code reads each value until it either finds a match or not. You could eliminate all those unnecessary comparisons and just do 1 comparison instead.

The second while loop could be written like below

while(<INPUT2>){
    chomp;
    my @current_line  = split /\t/;
    
    # eliminate unqualified lines early
    next unless $current_line[2] ==1 && $current_line[3] >= 3;
    
    if ($file1{ $current_line[0]}) {
        my ($lo, $hi) = @{ $file1{ $current_line[0] } };
        if ($lo <= $current_line[1] && $current_line[1] <= $hi) {
            print join("\t", $_, "***", $current_line[1]), "\n";
        }
    }
}

close (INPUT2);
[download]

In your input sample for file 2, only 3 of 24 lines qualified as valid, (column 3 == 1 and column 4 >= 3). Why not disqualify the 21 out of 24 lines before doing the other check (to see if column 1 is between the low and high ends of the range). That eliminates checking data (in your code) on lines that won't qualify anyway.

    # eliminate unqualified lines early
    next unless $current_line[2] ==1 && $current_line[3] >= 3;
[download]

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