187 void bcf_entry::set_indv_GENOTYPE_and_PHASE(unsigned int indv, const unsigned int &pos, const unsig…  in set_indv_GENOTYPE_and_PHASE()  argument
193 	ploidy[indv] = 0;  in set_indv_GENOTYPE_and_PHASE()
200 		ploidy[indv]++;  in set_indv_GENOTYPE_and_PHASE()
204 	if (ploidy[indv] == 0)  in set_indv_GENOTYPE_and_PHASE()
206 		set_indv_GENOTYPE_alleles(indv, make_pair(-2, -2));  in set_indv_GENOTYPE_and_PHASE()
208 	else if (ploidy[indv] == 1)  in set_indv_GENOTYPE_and_PHASE()
210 		set_indv_PHASE(indv, '|');  in set_indv_GENOTYPE_and_PHASE()
216 		set_indv_GENOTYPE_alleles(indv, make_pair(tmp, -2));  in set_indv_GENOTYPE_and_PHASE()
218 	else if (ploidy[indv] == 2)  in set_indv_GENOTYPE_and_PHASE()
231 			set_indv_PHASE(indv, '/');  in set_indv_GENOTYPE_and_PHASE()
237 			set_indv_PHASE(indv, phase);  in set_indv_GENOTYPE_and_PHASE()
239 		set_indv_GENOTYPE_alleles(indv, make_pair((int)tmp, (int)tmp2));  in set_indv_GENOTYPE_and_PHASE()
241 	else if (ploidy[indv] > 2)  in set_indv_GENOTYPE_and_PHASE()
243 	parsed_GT[indv] = true;  in set_indv_GENOTYPE_and_PHASE()
246 void bcf_entry::set_indv_GENOTYPE_and_PHASE(unsigned int indv, const pair<int, int> &genotype, char…  in set_indv_GENOTYPE_and_PHASE()  argument
248 	set_indv_GENOTYPE_ids(indv, genotype);  in set_indv_GENOTYPE_and_PHASE()
249 	set_indv_PHASE(indv, phase);  in set_indv_GENOTYPE_and_PHASE()
250 	parsed_GT[indv] = true;  in set_indv_GENOTYPE_and_PHASE()
253 void bcf_entry::set_indv_GENOTYPE_and_PHASE(unsigned int indv, const pair<string, string> &genotype…  in set_indv_GENOTYPE_and_PHASE()  argument
261 	set_indv_GENOTYPE_alleles(indv, a);  in set_indv_GENOTYPE_and_PHASE()
262 	set_indv_PHASE(indv, phase);  in set_indv_GENOTYPE_and_PHASE()
263 	parsed_GT[indv] = true;  in set_indv_GENOTYPE_and_PHASE()
266 void bcf_entry::set_indv_GENOTYPE_alleles(unsigned int indv, const pair<int, int> &in)  in set_indv_GENOTYPE_alleles()  argument
283 	GENOTYPE[indv] = in;  in set_indv_GENOTYPE_alleles()
284 	parsed_GT[indv] = true;  in set_indv_GENOTYPE_alleles()
287 void bcf_entry::set_indv_GENOTYPE_ids(unsigned int indv, const pair<int, int> &in)  in set_indv_GENOTYPE_ids()  argument
291 	GENOTYPE[indv] = in;  in set_indv_GENOTYPE_ids()
294 void bcf_entry::set_indv_PHASE(unsigned int indv, char in)  in set_indv_PHASE()  argument
299 	PHASE[indv] = in;  in set_indv_PHASE()
300 	parsed_GT[indv] = true;  in set_indv_PHASE()
303 void bcf_entry::set_indv_GQUALITY(unsigned int indv, const vector<char> &in)  in set_indv_GQUALITY()  argument
308 	parsed_GQ[indv] = true;  in set_indv_GQUALITY()
312 			GQUALITY[indv] = -1;  in set_indv_GQUALITY()
320 	GQUALITY[indv] = tmp;  in set_indv_GQUALITY()
323 void bcf_entry::set_indv_GQUALITY(unsigned int indv, const float &in)  in set_indv_GQUALITY()  argument
325 	parsed_GQ[indv] = true;  in set_indv_GQUALITY()
329 			GQUALITY[indv] = -1;  in set_indv_GQUALITY()
336 		GQUALITY[indv] = 99;  in set_indv_GQUALITY()
338 		GQUALITY[indv] = in;  in set_indv_GQUALITY()
341 void bcf_entry::set_indv_GFILTER(unsigned int indv, const vector<char> &in)  in set_indv_GFILTER()  argument
343 	parsed_FT[indv] = true;  in set_indv_GFILTER()
348 	GFILTER[indv].resize(0);  in set_indv_GFILTER()
367 			GFILTER[indv].push_back(ith_FILTER);  in set_indv_GFILTER()
376 		GFILTER[indv].push_back(ith_FILTER);  in set_indv_GFILTER()
379 void bcf_entry::set_indv_GFILTER(unsigned int indv, const string &in)  in set_indv_GFILTER()  argument
381 	parsed_FT[indv] = true;  in set_indv_GFILTER()
386 	GFILTER[indv].resize(0);  in set_indv_GFILTER()
401 		GFILTER[indv].push_back(ith_FILTER);  in set_indv_GFILTER()