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nucular v. 050222

CITATION

  If you use nucular, pleace cite the following:

	Lemire M (2005) A simple non-parametric procedure to test for linkage
	through mothers or fathers as well as imprinting in the presence
	of linkage. BMC Genet. (in press).
 
NAME
        nucuclar - a program that splits extended pedigrees into nuclear
	families, with the option of recoding all sibs as half-sibs with 
	distinct mothers of fathers.	

SYNOPSIS
        nucular [options] [pedfile]

DESCRIPTION

	Used without an option, nucular splits all the extended pedigrees
	(in standard linkage format) into distinct nuclear families (ie
	both parents of the sibship become founders).  A file with the
	name <nucular_[pedfile]> is created.

	-f 
		Splits as above, but make all full sibs into half-sibs, with 
		distinct fathers.  A file <dummyf_nucular_[pedfile]> is 
		created.

	-m
		Same as -f, but with distinct mothers. A file 
		<dummym_nucular_[pedfile]> is created.

INPUT FILES
	
	A standard pre-makefile pedigree file. Only the pedigree ID column is 
	allowed to be a character string. All other columns must contain integer
	values (a csh script is provided in this distribution to recode the IDs
	into integer values. See Test/README.tests for details).


INCLUDED FILES
	
	GNUGeneralPublicLicense.txt
	Makefile
	PedStruct.cc
	PedStruct.hh
	PedStruct.o
	PedStructByFam.cc
	PedStructByFam.hh
	PedStructByFam.o
	PedStructByNuclearFam.cc
	PedStructByNuclearFam.hh
	PedStructByNuclearFam.o
	README
	Test/README.tests
	Test/dummyf_nucular_test.ped
	Test/dummym_nucular_test.ped
	Test/nucular_test.ped
	Test/recoded__test.ped
	Test/test.ped
	nucular.cc
	recodeID.csh

        Compiles under Solaris 8 (gcc 2.95.3), Linux (gcc 3.3.2)

AUTHOR
        Written by Mathieu Lemire, 
	McGill University and Genome Quebec Innovation Centre

	Version 050222 (22 February 2005).  Distribution version 0.0.
        
	Code written in C/C++.


COPYRIGHT
        nucular -- a program that splits extended pedigrees into nuclear families
        Copyright (C) 2005 Mathieu Lemire.

        This program is 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 or 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; if not, write to the Free Software Foundation,
        Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.


CONTACT
        Mathieu Lemire
        mlemire [at] sdf dot lonestar dot org