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assemble_direct, sequence too short

  • Hi, is there any way to bypass this error on assemble_direct.  I would *really* like to have all my reads with AP tags entered into the database, even if they are too short.  Why isn't there an enter_failures option on assemble_direct?  Thanks. 

    Cristyn Bromberg
    Broad Institute of MIT and Harvard
    320 Charles St, Cambridge MA 02141

    • James Bonfield
      James Bonfield

      A cursory glance at the code indicates that "too short" means zero basepairs. Do you *really* want zero length sequences assembled in? It's not something gap4 handles and they are reported as errors by Check Database.

      Please  check the SL/SR and QL/QR values in the files being rejected. If you have a case that isn't apparently zero length then I'll investigate this further of course.