[Bioperl-l] Fasta Qual files

hilmar.lapp@pharma.Novartis.com hilmar.lapp@pharma.Novartis.com
Thu, 14 Sep 2000 19:00:19 +0100

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


     $qual_str = reverse($qual_str);


     $qual_str = substr($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).