Problems with PREPLINK

Daniel E. Weeks dweeks at WATSON.HGEN.PITT.EDU
Tue Jul 7 09:24:10 EST 1992


Ellen Wijsman and Heikki Lehvaslaiho both have had
problems with preplink on the SUN.

Heikki Lehvaslaiho sent me the following example:

**********************************************************************
The following outfile from preplink illustrates the problem. The first row
of penetrances was typed in as:

 0.0000 0.1500 0.6000

Next time the screen is updated 0.15 has converted to 0.
__________________________________________________________________
 2 0 0 5  << NO. OF LOCI, RISK LOCUS, SEXLINKED (IF 1) PROGRAM
 0 0.0 0.0 0  << MUT LOCUS, MUT RATE, HAPLOTYPE FREQUENCIES (IF 1)
  1  2
1   2  << AFFECTION, NO. OF ALLELES
 0.999000 0.001000   << GENE FREQUENCIES
 4 << NO. OF LIABILITY CLASSES
 0.0000 0.0000 0.6000
 0.0000 0.4000 0.7500
 0.0000 0.7000 0.9000
 0.0000 0.9000 0.9500 << PENETRANCES
3   7  << ALLELE NUMBERS, NO. OF ALLELES
 0.140000 0.140000 0.140000 0.160000 0.140000 0.140000 0.140000   <<
GENEFREQ
   1 0.05 0.4
 0.2 0.1 0.5
__________________________________________________________________
**********************************************************************


The solution to the problem is simple:  The constant determining
the maximum number of liability classes is set to 3:
  maxliab = 3;                  {MAXIMUM NUMBER OF LIABILITY CLASSES }

So when 4 liability classes are tried, preplink does bizarre
things.

This points out a general problem with the LINKAGE programs: They
are not compiled to check for range errors when they are distributed.
However, on the SUN, this can be accomplished in the following manner:
 pc -C -L -o preplink preplink.p

To avoid such problems, I suggest changing all the Makefiles to
include the '-C' option and then recompiling ALL the LINKAGE programs.

Sincerely,
 -- Dan Weeks --

********************************
| Daniel E. Weeks              | 
| Department of Human Genetics |  Internet: 
| University of Pittsburgh     |    dweeks at watson.hgen.pitt.edu
| Crabtree Hall, Room A310     |
| 130 DeSoto Street            |  Bitnet:
| Pittsburgh, PA 15261         |    weeks at pittvms.bitnet
|                              |
| (412) 624-3066               |
| FAX: (412) 624-3020          |
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