From:	GOLD::BITNET%"FUCHS@EMBL.BITNET"      "Rainer Fuchs " 18-DEC-1989 13:06
To:	Don Gilbert <GILBERTD@IUBACS.BITNET>
Subj:	GCG bugs (I)

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Date:         Thu, 14 Dec 89 12:26:00 N
Reply-To:     "Rainer Fuchs (EMBL)" <FUCHS@EMBL>
Sender:       "INFO-GCG: Univ. of Wisconsin Genetics Analysis Software
              Discussion" <INFO-GCG@UTORONTO>
From:         "Rainer Fuchs (EMBL)" <FUCHS@EMBL.BITNET>
Subject:      GCG bugs (I)
To:           Don Gilbert <GILBERTD@IUBACS.BITNET>
 
 I forward to bug reports and fixes of the GCG package:
 
> Dear GCG users,
>
> One of our users of the GCG program package has found an error in the program
> BESTFIT:
> In the output the sequence numbers for the reverse sequence have been
> incorrect.
>
> We wrote to GCG about it and received the following answer which enabled us to
> fix the bug:
>
> ------------------------------------------------------------------------------
   -
> In Version 6.1 of the GCG package, we accidentally introduced a bug in
> attempting to fix another bug.  I'll describe the steps required to fix this
> new bug.
>
> 1) Initialize GCG and GCGSupport with the following:
> $ GCG
> $ GCGSupport
>
> 2) Copy the source code for GAP (BESTFIT is really GAP with the /BESTFIT comma
   nd
>
> line switch) to your default scratch directory with the following:
> $ Take Gap Mod
>
> 3) Edit the file Gap.For and search for the text "fixes numbering".  You shoul
   d
> see the following lines:
>
> ! fixes numbering problem with reversed sequence in BESTFIT
>
>             If ( Seq1Rev ) Start1=Seq1End-Off1-StrCount(s1,'~.',-1)+1
>             If ( Seq2Rev ) Start2=Seq1End-Off2-StrCount(s2,'~.',-1)+1
>
> 4) In the second line of code listed above, change Seq1End to be Seq2End.  The
   se
>
> lines should then read as follows:
>
> ! fixes numbering problem with reversed sequence in BESTFIT
>
>             If ( Seq1Rev ) Start1=Seq1End-Off1-StrCount(s1,'~.',-1)+1
>             If ( Seq2Rev ) Start2=Seq2End-Off2-StrCount(s2,'~.',-1)+1
>
> 5) Save this modified file and then place the modified source code back in its
> appropriate directory with the following:
> $ Save Gap
>
> 6) Compile and link the modified code with the following:
> $ Make Gap
>
> The bug should now be fixed.  If you need any clarification, please ask.
>
> Sincerely,
> Irv Edelman
> Bitnet: Edelman@WiscPSL
> (608)263-8970
> ------------------------------------------------------------------------------
   -
>
> I hope this information is useful for you.
>
> Best regards
> Clemens
>
> ------------------------------------------------------------------------------
   -
>  Clemens Broger, Ph. D.                       Phone: +41-61-688-4447
>                                                Post: Central Research Units
>  Please reply to:                                    F.Hoffmann-La Roche Ltd.
>  BrogerC%Roche.Basel.EMBnet.CH@EMBL.bitnet           CH-4002 Basel, Switzerlan
   d
> ------------------------------------------------------------------------------
   -
 
 
 Rainer Fuchs, Ph.D.
 EMBL Data Library
 fuchs@embl.bitnet