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//////////////////////////////////////////////////////////////////
// //
// PLINK (c) 2005-2006 Shaun Purcell //
// //
// This file is distributed under the GNU General Public //
// License, Version 2. Please see the file COPYING for more //
// details //
// //
//////////////////////////////////////////////////////////////////
#ifndef __HAPWINDOW_H_
#define __HAPWINDOW_H__
class HaploPhase;
class Plink;
class MultiLocusGenotype;
class HaploWindow
{
public:
int ns; // Number of SNPs in haplotype
int nh; // Number of possible haplotypes
int np; // Number of phases, diploid
// Parent 'region', PLINK
HaploPhase * haplo;
Plink * P;
// Start and stop positions (relative to region)
int start, stop;
// Haplotype frequencies
vector_t f;
// Window haplotype codes
vector<vector<bool> > hap;
// Stub codes for each haplotype (for quick lookup)
vector<int> leftStub;
vector<int> rightStub;
// Lookup table for haplotype number given SNPs
map<vector<bool>,int> hapmap;
// List of SNP numbers
intvec_t S;
// Posterior probabilities, per individual
matrix_t pp;
// Haplotype phases, per individual
table_t hap1;
table_t hap2;
// Ambiguous for this window?
boolvec_t ambig;
// Unamiguous haplotype counts
vector_t uc;
// Store count, reference individual
set<MultiLocusGenotype*> genotypes;
// Store which genoGroup a person belongs to
vector<MultiLocusGenotype*> genoGroup;
// Finished with this window?
bool converged;
bool left_passed;
bool right_passed;
// Convergence
vector<bool> zero;
double sampleLogLikelihood;
int iter;
///////////////////////////////
// Functions
HaploWindow(HaploPhase *, Plink *);
~HaploWindow();
void expandGenogroups();
void enumerateGenogroups();
void pruneGenogroups(double t=par::haplo_plem_window_prune_phase);
void enumerateHaplotypes(intvec_t &);
void setStubCodes();
void performEM();
void enumeratePhase(int);
void prunePhase(int,double t=par::haplo_plem_window_prune_phase);
void reportPhase();
string haplotypeName(int i);
// Get overlap frequency from a window
vector_t leftStubFrequency();
vector_t rightStubFrequency();
void tallyUnambiguousCounts();
};
#endif
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