> sub readDefectData {
>         my $defectDataFH=new FileHandle;
>         open ($defectDataFH,$_[0]) or die "Error: Cannot load defectivity
> data, $_[0]\n";
>         print "Loading defect data ... ";
>         my %short;
>         while ($_=$defectDataFH->getline) {
>                 chomp;
>                 print "P8: $_\n";
>                 @_=split (/ /,$_);
>                 print "P9: @_\n";
>                 if ($_[0]=~/SHORT/) {
>                   .... # performs some initializing kind of stuff and
> returns a hash to the caller.
>                 }
> }
> 
> sub readLayerMap {
> }

readDefectData has unbalanced braces...

As far as coding style goes, I would suggest keeping everything as
simple and generic as possible for maximum reusability. Also, code
defensively and make sure you have a way to turn on lots of debug
information about *exactly* what is happening when your code runs.
Data::Dumper is your friend.

One reason to choose perl over C/C++ is that you don't really have to.
If you need to, you can call out to C using the XS interface if you
find bottlenecks that are unacceptable. Premature optimization is the
root of all evil.

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