[Biopython-dev] [Bug 2848] New: SeqIO fastq routines reject valid quality socres

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2848

           Summary: SeqIO fastq routines reject valid quality socres
           Product: Biopython
           Version: 1.50
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: pmmagic at gmail.com


The fastq routines in SeqIO.QualityIO reject what I believe are valid quality
scores.

According to the MAQ website (http://maq.sourceforge.net/fastq.shtml; I don't
know if this is definitive), valid quality values in Sanger style FASTQ format
are:

<qual>  :=      [!-~\n]+

This corresponds to Phred quality scores in the range 0-93.

The current code in BioPython 1.50 rejects quality scores > 90.


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