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/*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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 3 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, see <http://www.gnu.org/licenses/>.
*/
#ifndef __GENOTYPE_ELIMINATION__
#define __GENOTYPE_ELIMINATION__
#include "Pedigree.h"
class GenotypeList
{
public:
IntArray allele1, allele2;
IntArray alleles;
bool ignore;
int checked;
GenotypeList();
static bool EliminateGenotypes(Pedigree & ped, Family * family, int marker);
void Dimension(int genotypes);
void Delete(int genotype);
bool Matches(int genotype, int allele);
bool Matches(int allele);
int SaveGenotype(int genotype);
void SetGenotype(int genotype, int al1, int al2);
private:
static void InitializeList(GenotypeList * list, Pedigree & p, Family * f, int marker);
static bool PairwiseCheck(GenotypeList * list, Pedigree & p, Family * f);
static bool FamilyCheck(GenotypeList * list, Pedigree & p, Family * f);
static bool CheckTrio(GenotypeList * list, int fatid, int motid, int child, int i, int j, int k);
static bool TrimParent(GenotypeList * list, Person & person, int fatid, int motid);
static bool Cleanup(GenotypeList * list, Person & person, int fatid, int motid, int child, int geno);
static void Print(GenotypeList * List, Pedigree & p, Family * f, int marker);
};
#endif
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