#11 Order contigs does not work

V1.4.1
closed-fixed
Gap4 (50)
2
2004-08-05
2004-05-20
HolgerW
No

Unfortunately, I found that Order Contigs does not work
in version 1.4.1.

Regards,

Holger Wedler

holger.wedler@freenet.de

Discussion

  • HolgerW

    HolgerW - 2004-05-20
    • assigned_to: nobody --> jkbonfield
     
  • James Bonfield

    James Bonfield - 2004-05-24
    • priority: 5 --> 2
     
  • James Bonfield

    James Bonfield - 2004-05-24

    Logged In: YES
    user_id=154581

    Can you be more specific please? It is true that there are
    times where Order Contigs makes a total hash up of things.
    It's like an assembly problem and the algorithm used isn't
    ideal so there will always be times when it doesn't find the
    optimal solution.

    If it's not crashing, but simply not being optimal, then I
    consider this bug to be a request for an improved algorithm.

    James

     
  • Schlagenhauf Edith

    Logged In: YES
    user_id=188694

    To be more specific, I also got the following error message:

    UpdateAutomaticContigOrder couldn't read file
    "/usr/local/staden-linux-1-4-1/linux-bin/../lib/gap/contig_order.tcl":
    no such file or directory

    putting the contig_order.tcl file from Staden2002.0 version into
    the appropriate directory apparently fixed the problem.

    Edith Schlagenhauf
    ediths@botinst.unizh.ch

     
  • James Bonfield

    James Bonfield - 2004-08-05
    • status: open --> closed-fixed
     
  • James Bonfield

    James Bonfield - 2004-08-05

    Logged In: YES
    user_id=154581

    Thanks for spotting this problem. For some reason this file
    was missing from CVS too, but it was in my own source tree.

    I've added it as a separate download to the 1.4.1 file
    release and will make sure that it arrives in the next full
    release.

    James

     

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