[Biopython-dev] [Bug 2905] New: Short read alignment format

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2905

           Summary: Short read alignment format
           Product: Biopython
           Version: 1.51
          Platform: All
        OS/Version: Mac OS
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: osvaldo.zagordi at bsse.ethz.ch


Hi again,
is there any plan to develop some parsers for alignment of short reads? There's
a lot of formats around, and the most serious proposal for a format I've seen
is SAM (http://samtools.sourceforge.net/). I should start writing something to
parse this output soon. Any suggestion on where to start from (in order not to
depend on some module that will be soon obsolete)?

Thanks,
    Osvaldo


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