README for  Modified GENEHUNTER/Kong&Cox Package.
October 24, 2005

This package contains modified versions of asm.tar.gz and
ghp-1.2.tar.gz, (and versions of the programs asm, ghp, and xghp for
execution under either Solaris or WINDOWS/cygwin) as developed and
distributed by Kong and Cox [1].  Except as noted below, these programs
are used in exactly the same way as the original versions.

Only the files ghmain.c, finalprep.c, Xfnalprep.c, and nplscore.c
have been changed.  For these changes we have used files 2include.h and
2auuxx.c, which are largely versions of material from Numerical Recipes in
C, but which also include small utility routines.  Alternate versions of
ansilib/asm.h and ansilib/syscode.c are provided to facilitage compilation
under WINDOWS/cygwin.  They differ slightly from the original asm.h
and syscode.c.  The file,  values.h, is added by us because it is needed
for the compilation of asm under WINDOWS/cygwin.

We have replaced the example data provided by Kong and Cox with other
example data, contained in the files mdatw, pdatw, wghts.dat, and in
the GeneHunter command file, ghp CommandFile. For x-linked data, the
example files xgen.loc and xgen.ped are those distributed by Kong and
Cox.  [Note: the pedigree data format for use with our programs  must
include a column for liability class,  even if there is only one
liability class.  xgen.ped-as distributed by Kong and Cox does not have
this column. It should be added to xgen.ped before using xgen.ped with
our programs.]

The executable versions of ghp and xghp were compiled from the
GENEHUNTER-PLUS sources as altered by us. They extend GENEHUNTER-PLUS
to allow weights, and so they differ from the ghp and xghp distributed
by Kong and Cox.  The compilations of ghp and xghp were done on a
(64-bit) system running Solaris 2.8 kernel=Generic_117350-24 by gcc
version-3.2.

As described in the INSTALL.ghp  note, it is possible to compile
executables for other operating systems with little or no changes to
the source files.  To compile for WINDOWS/cygwin using gcc: a)change
-D_SYS_SOLARIS to -D_SYS_OSF; and  b)copy ansilib/syscode.h.windows to
ansylib/syscode.h and ansilib/syscode.c.windows to ansilib/syscode.c.
We also include in this package executables, for asm, ghp, and xghp
which will run when called from a WINDOWS command window when cygwin
has been installed.

To run the modified version of xghp or ghp, you need a file named
wghts.dat in the directory from which the call to ghp is made.  This
file must be an ordinary text file having no empty lines except
possibly at the end. It must contain on each line a single number, the
weight, for each (line) individual in the pedigree file.

The files asm, ghp, and xghp are the Kong&Cox extensions to gh-1.3
NOTE: xgh is in (GeneHunter)gh-1.3:  IT IS NOT in gh-v2_1...  Although
gh-v2_1 is 10-1000 times faster than gh-1.3, faster implementations of
the calculations for the Kong&Cox statistics
 are done in the package Allegro (2) which is not as freely available
 as gh-1.3.



References
1) Allele-Sharing Models: LOD Scores and Accurate Linkage tests;
    Augustine Kong and Nancy J. Cox(1997); Am. J. Hum. Genet. 61:1179-1188.
2) Allegro version 2;Gudbjartsson, Thorvaldsson, Kong, Gunnarsson,
    Ingolfsdottir (2005); Nature Genetics, 37:1015-1016.