comment on

too much code , too many file system operations

Where is the problem?

Is the problem with the data structure , or the subroutine doing the printing?

When you Data::Dump::dd()umper up the data structure and read it with your eyes, is everything there?

If you really want more help, you should whittle down your program to this

my %ref;
my $threelinefakein = "...\n...";
fillRef( \%ref, \$threelinefakein );

my @fakes = ( "1\n2\n3", "1\n2\n3" );
for my $fake ( @fakes ){

   refLogic( \%ref, \$fake );
}
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subroutines save the day, its very easy to debug subroutines, you don't need files on the harddisk and other stuff we don't have (and don't really want :)

Here is how you might start writing refLogic and fillRef

## Usage: fillRef( $hashref, $infilename );
sub fillRef {
## so you can keep using $ref{blah}
## less rewriting when you copy/paste
   local *ref = shift;
## open the string as file
   open IN, '<', shift;
   ...
}


## Usage: refLogic( $hashref, $infilename );
sub refLogic {
   local *ref = shift;
## open the string as file
   open IN, '<', shift;
## fake out for testing
   local *OUT = \*STDOUT;
}
[download]

Eliminate file system operations for files we don't have, include three lines files that replicate the problem, include them as strings

update: finally I read the whole thing you posted, just dumper up two variables and we can start debugging these two loops

    my %ref    = ... ; ## Data::Dump::dd(%ref)    output here
    my @probes = ... ; ## Data::Dump::dd(@probes) output here
##
    foreach my $key ( sort keys %ref ) {

        #intended function
        print OUT $ref{$key} . "\t" . $probes[$key];

        #testing
        my @temp = split "\t", $ref{$key};
        foreach (@temp) {
            if ( $temp[0] == 2 ) {
                print $key. "\t" . $ref{$key} . "\t" . $probes[$key];
            }
        }
    }
##
    foreach my $key ( sort keys %ref ) {
        print OUT $ref{$key} . "\t" . $probes[$key];
        my @temp = split "\t", $ref{$key};
        foreach (@temp) {
            if ( $temp[0] == 2 ) { print $key. "\t" . $ref{$key} . "\n
+"; }
        }
    }

[download]

update: now that I've looked at these two loops, well, the inner foreach is completely unneeded .... and aside from the different things you print (one has probles the other doesn't), they're pretty much the same thing

Hope this help, if it doesn't, well, take a break, post short code, we'll figure it out

	For:		Use:
	&		`&`
	<		`<`
	>		`>`
	[		`[`
	]		`]`