[Bioperl-l] Fasta Qual files

[hilmar.lapp@pharma.Novartis.com]

>   my @qual = (40,34,35,99,99);
>   my $qual_str = pack('C*', @qual);
>   @qual = unpack('C*', $qual_str);
>

Reversal:

     $qual_str = reverse($qual_str);

Truncation:

     $qual_str = substr($qual_str, 0, 3);

<someone being forced to use an email client full of bells and whistles but
lacking support for quoting -- because you can simply use color - what a
great idea -- trying to indicate where his scribble begins>

   I see. As you see I'm not so familiar with Perl guts. I was able to
   verify that 0s are correctly retained (and don't terminate a string),
   but negative values obviously lose their original values. Negative
   values do occurr in quality values, at least in Phred/Phrap. What about
   signed chars? Are there quality values beyond 127? The highest value
   used by Phred/Phrap is 100. (BTW you can obviously convert 'high' values
   back to their original negative representations, but you'd still have to
   make an assumption about the highest possible quality value).

      Hilmar