perl fq_all2std.pl instruction

FASTQ format is first used in the Sanger Institute, and therefore
we take the Sanger specification as the standard FASTQ. Although
Solexa/Illumina reads file looks pretty much like the standard
FASTQ, they are different in that the qualities are scaled
differently. In the quality string, if you can see a character
with its ASCII code higher than 90, probably your file is in the
Solexa/Illumina format.

Sometimes we also use an integer, instead of a single character,
to explicitly show the qualities. In that case, negative
qualities indicates that Solexa/Illumina qualities are used.

sub sol2std {
  my $max = 0;
  while (<>) {
	if (/^@/) {
	  
          # print the first entry line
          print;
	 
          # print the seq line, skip the second ID line and 
          # get the content of the quality line

	  # the actual problem is there, the carriage return 
          # char is captured as well	  
          $_ = <>; print; $_ = <>; $_ = <>;
          
          # my solution is to add this line:
          #  chomp;	  
          my @t = split('', $_);

          # here the at array contains all the quality 
          # chars + a carriage return 
 	  my $qual = '';

          # here the additional carriage return will be converted 
          # as well; therefore the ! which is introduced
	  $qual .= $conv_table[ord($_)] for (@t);
	  print "+\n$qual\n";
	}
  }
}

maq sol2sanger