Case Control tests for Samples with Related Individuals (CC-QLS)
 Copyright(C) 2003 Catherine Bourgain, Carole Ober, Mary Sara McPeek 
Homepage: http://galton.uchicago.edu/~mcpeek/software/CCQLSpackage1.3/index.html
Release 1.3.  March 11,2006

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License

This program is a free software; you can redistribute it and/or 
modify it under the terms of the GNU General Public License 
as published by the Free Software Foundation; either version 2 
of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY of FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
General Public License for more details.

You should have received a copy of the GNU General Public License 
along with this program (see file gpl.txt); if not, write to the 
Free Software Foundation, Inc., 59 Temple Place - Suite 330, 
Boston, MA 02111-1307, USA.

We request that use of this software be cited in publications as 
Bourgain, Hoffjan, Nicolae, Newman, Steiner, Walker, Reynolds, Ober 
and McPeek (2003). Novel Case-Control Test in a Founder Population 
Identifies P-selectin as an Atopy Susceptibility Locus, 
American Journal of Human Genetics 73:612-626

To contact the author:
Catherine Bourgain
INSERM U535
Bat.Leriche
Hopital Paul Brousse
BP 1000
94817 Villejuif Cedex
France
Tel : +33 1 45 59 53 85
Fax : +33 1 45 59 53 31
bourgain@vjf.inserm.fr

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Installation instructions:

1.  Download the CC-QLS package which includes the 'CC-QLStest.c' program.
    
2.  Read the files 'Overview', 'Input', 'Output' and 'Tips' carefully
    to understand the purpose of this program and how it works.
  
3.  Edit the 'Makefile' as necessary according to the instructions in
    the 'Makefile'.  You should only need to make sure that the correct
    compiler and compiler options for your machine are chosen.

4.  Type 'make'.  This will build an executable program 'CC-QLStest'.

5.  To run the executable program 'CC-QLStest':

    First, prepare the input files, e.g., 'markid'
    and 'kinshipcoef' (see the files 'Example' and 
    'Input' for more details).

    Then, type ./CC-QLStest markid kinshipcoef

6.  Results are output in a file called 'CC-QLStest.out'. Warnings may
    also be printed in a 'CC-QLStest.err' file.
  
7.  You can test the executable program 'CC-QLStest' by running it 
    with two different sets of input files :
    - 'markid_Hutt' and 'kinshipcoef_Hutt' corresponding to data from a single 
       large inbred pedigree (2 markers)
    - 'markid_Sib' and 'kinshipcoef_Sib' corresponding to data from independent outbred 
       nuclear families
    You can then compare your output in the file 'CC-QLStest.out' with 
    the correct output in the sample output files 'Hutt_CC-QLStest.out' or 'Sib_CC-QLStest.out'

9.  The programs stop if any errors are detected in the format of the 
    input files.