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Searched refs:populationTarget (Results 1 – 25 of 35) sorted by relevance

12

/dports/biology/vcflib/vcflib-1.0.2/src/
H A DpFst.cpp276 zvar * populationTarget ; in main() local
311 delete populationTarget; in main()
323 delete populationTarget; in main()
336 populationTarget->alpha = 0.001 + populationTarget->nref; in main()
337 populationTarget->beta = 0.001 + populationTarget->nalt; in main()
346 …le populationTargetEstAF = bound(populationTarget->beta / (populationTarget->alpha + … in main()
352 …double null = logLbinomial(populationTarget->beta, (populationTarget->alpha + populationTarget->be… in main()
354 …double alt = logLbinomial(populationTarget->beta, (populationTarget->alpha + populationTarget->be… in main()
360 delete populationTarget; in main()
380 delete populationTarget; in main()
[all …]
H A DwcFst.cpp248 genotype * populationTarget ; in main() local
252 populationTarget = new pl(); in main()
256 populationTarget = new gl(); in main()
260 populationTarget = new gp(); in main()
264 populationTarget = new gt(); in main()
272 delete populationTarget; in main()
277 delete populationTarget; in main()
282 delete populationTarget; in main()
290 delete populationTarget; in main()
309 s2 += ((populationTarget->ngeno * pow(populationTarget->af - pbar, 2))/nbar); in main()
[all …]
H A DpopStats.cpp234 genotype * populationTarget ; in main() local
238 populationTarget = new pl(); in main()
241 populationTarget = new gl(); in main()
244 populationTarget = new gp(); in main()
260 if(populationTarget->af == -1){ in main()
261 delete populationTarget; in main()
265 double ehet = 2*(populationTarget->af * (1 - populationTarget->af)); in main()
268 << populationTarget->af << "\t" in main()
270 << populationTarget->hfrq << "\t" in main()
271 << populationTarget->nhet << "\t" in main()
[all …]
H A DgenotypeSummary.cpp330 genotype * populationTarget ; in main() local
333 populationTarget = new pl(); in main()
336 populationTarget = new gl(); in main()
339 populationTarget = new gp(); in main()
342 populationTarget = new gt(); in main()
348 if(populationTarget->genoIndex[i] == -1){ in main()
351 else if (populationTarget->genoIndex[i] == 0) { in main()
358 else if (populationTarget->genoIndex[i] == 1){ in main()
361 else if (populationTarget->genoIndex[i] == 2) { in main()
370 cerr << populationTarget->genoIndex[i] << endl; in main()
[all …]
H A DvcfToHap.cpp397 genotype * populationTarget ; in main() local
400 populationTarget = new pl(); in main()
403 populationTarget = new gl(); in main()
406 populationTarget = new gp(); in main()
409 populationTarget = new gt(); in main()
414 if(populationTarget->af <= globalOpts.af || populationTarget->af >= (1-globalOpts.af) ){ in main()
415 delete populationTarget; in main()
419 afs.push_back(populationTarget->af); in main()
420 loadPhased(haplotypes, populationTarget, populationTarget->gts.size()); in main()
422 populationTarget = NULL; in main()
[all …]
H A DiHS.cpp621 genotype * populationTarget ; in main() local
624 populationTarget = new pl(); in main()
627 populationTarget = new gl(); in main()
630 populationTarget = new gp(); in main()
633 populationTarget = new gt(); in main()
639 || populationTarget->nref < 2 in main()
640 || populationTarget->nalt < 2){ in main()
641 delete populationTarget; in main()
646 loadPhased(haplotypes, populationTarget, populationTarget->gts.size()); in main()
648 populationTarget = NULL; in main()
[all …]
H A DplotHaps.cpp354 genotype * populationTarget ; in main() local
357 populationTarget = new pl(); in main()
360 populationTarget = new gl(); in main()
363 populationTarget = new gp(); in main()
366 populationTarget = new gt(); in main()
369 populationTarget->loadPop(target, var.sequenceName, var.position); in main()
372 afs.push_back(populationTarget->af); in main()
373 loadPhased(haplotypes, populationTarget, populationTarget->gts.size()); in main()
H A DsequenceDiversity.cpp423 genotype * populationTarget ; in main() local
428 populationTarget = new pl(); in main()
433 populationTarget = new gl(); in main()
438 populationTarget = new gp(); in main()
443 populationTarget = new gt(); in main()
448 populationTarget->loadPop(target, var.sequenceName, var.position); in main()
456 delete populationTarget; in main()
462 targetAFS.push_back(populationTarget->af); in main()
/dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/
H A DpFst.cpp254 zvar * populationTarget ; in main() local
289 delete populationTarget; in main()
301 delete populationTarget; in main()
314 populationTarget->alpha = 0.001 + populationTarget->nref; in main()
315 populationTarget->beta = 0.001 + populationTarget->nalt; in main()
324 …le populationTargetEstAF = bound(populationTarget->beta / (populationTarget->alpha + … in main()
330 …double null = logLbinomial(populationTarget->beta, (populationTarget->alpha + populationTarget->be… in main()
332 …double alt = logLbinomial(populationTarget->beta, (populationTarget->alpha + populationTarget->be… in main()
338 delete populationTarget; in main()
358 delete populationTarget; in main()
[all …]
H A DwcFst.cpp239 genotype * populationTarget ; in main() local
243 populationTarget = new pl(); in main()
247 populationTarget = new gl(); in main()
251 populationTarget = new gp(); in main()
255 populationTarget = new gt(); in main()
263 delete populationTarget; in main()
268 delete populationTarget; in main()
273 delete populationTarget; in main()
281 delete populationTarget; in main()
300 s2 += ((populationTarget->ngeno * pow(populationTarget->af - pbar, 2))/nbar); in main()
[all …]
H A DpopStats.cpp222 genotype * populationTarget ; in main() local
226 populationTarget = new pl(); in main()
229 populationTarget = new gl(); in main()
232 populationTarget = new gp(); in main()
248 if(populationTarget->af == -1){ in main()
249 delete populationTarget; in main()
253 double ehet = 2*(populationTarget->af * (1 - populationTarget->af)); in main()
256 << populationTarget->af << "\t" in main()
258 << populationTarget->hfrq << "\t" in main()
259 << populationTarget->nhet << "\t" in main()
[all …]
H A DgenotypeSummary.cpp320 genotype * populationTarget ; in main() local
323 populationTarget = new pl(); in main()
326 populationTarget = new gl(); in main()
329 populationTarget = new gp(); in main()
332 populationTarget = new gt(); in main()
338 if(populationTarget->genoIndex[i] == -1){ in main()
341 else if (populationTarget->genoIndex[i] == 0) { in main()
348 else if (populationTarget->genoIndex[i] == 1){ in main()
351 else if (populationTarget->genoIndex[i] == 2) { in main()
360 cerr << populationTarget->genoIndex[i] << endl; in main()
[all …]
H A DvcfToHap.cpp388 genotype * populationTarget ; in main() local
391 populationTarget = new pl(); in main()
394 populationTarget = new gl(); in main()
397 populationTarget = new gp(); in main()
400 populationTarget = new gt(); in main()
405 if(populationTarget->af <= globalOpts.af || populationTarget->af >= (1-globalOpts.af) ){ in main()
406 delete populationTarget; in main()
410 afs.push_back(populationTarget->af); in main()
411 loadPhased(haplotypes, populationTarget, populationTarget->gts.size()); in main()
413 populationTarget = NULL; in main()
[all …]
H A DiHS.cpp607 genotype * populationTarget ; in main() local
610 populationTarget = new pl(); in main()
613 populationTarget = new gl(); in main()
616 populationTarget = new gp(); in main()
619 populationTarget = new gt(); in main()
625 || populationTarget->nref < 2 in main()
626 || populationTarget->nalt < 2){ in main()
627 delete populationTarget; in main()
632 loadPhased(haplotypes, populationTarget, populationTarget->gts.size()); in main()
634 populationTarget = NULL; in main()
[all …]
H A DmeltEHH.cpp592 genotype * populationTarget ; in main() local
595 populationTarget = new pl(); in main()
598 populationTarget = new gl(); in main()
601 populationTarget = new gp(); in main()
604 populationTarget = new gt(); in main()
610 || populationTarget->nref < 2 in main()
611 || populationTarget->nalt < 2){ in main()
612 delete populationTarget; in main()
617 loadPhased(haplotypes, populationTarget, populationTarget->gts.size()); in main()
619 populationTarget = NULL; in main()
[all …]
H A DplotHaps.cpp346 genotype * populationTarget ; in main() local
349 populationTarget = new pl(); in main()
352 populationTarget = new gl(); in main()
355 populationTarget = new gp(); in main()
358 populationTarget = new gt(); in main()
361 populationTarget->loadPop(target, var.sequenceName, var.position); in main()
364 afs.push_back(populationTarget->af); in main()
365 loadPhased(haplotypes, populationTarget, populationTarget->gts.size()); in main()
H A DsequenceDiversity.cpp413 genotype * populationTarget ; in main() local
418 populationTarget = new pl(); in main()
423 populationTarget = new gl(); in main()
428 populationTarget = new gp(); in main()
433 populationTarget = new gt(); in main()
438 populationTarget->loadPop(target, var.sequenceName, var.position); in main()
446 delete populationTarget; in main()
452 targetAFS.push_back(populationTarget->af); in main()
/dports/biology/freebayes/freebayes-1.3.5/vcflib/src/
H A DpFst.cpp254 zvar * populationTarget ; in main() local
289 delete populationTarget; in main()
301 delete populationTarget; in main()
314 populationTarget->alpha = 0.001 + populationTarget->nref; in main()
315 populationTarget->beta = 0.001 + populationTarget->nalt; in main()
324 …le populationTargetEstAF = bound(populationTarget->beta / (populationTarget->alpha + … in main()
330 …double null = logLbinomial(populationTarget->beta, (populationTarget->alpha + populationTarget->be… in main()
332 …double alt = logLbinomial(populationTarget->beta, (populationTarget->alpha + populationTarget->be… in main()
338 delete populationTarget; in main()
358 delete populationTarget; in main()
[all …]
H A DwcFst.cpp239 genotype * populationTarget ; in main() local
243 populationTarget = new pl(); in main()
247 populationTarget = new gl(); in main()
251 populationTarget = new gp(); in main()
255 populationTarget = new gt(); in main()
263 delete populationTarget; in main()
268 delete populationTarget; in main()
273 delete populationTarget; in main()
281 delete populationTarget; in main()
300 s2 += ((populationTarget->ngeno * pow(populationTarget->af - pbar, 2))/nbar); in main()
[all …]
H A DpopStats.cpp222 genotype * populationTarget ; in main() local
226 populationTarget = new pl(); in main()
229 populationTarget = new gl(); in main()
232 populationTarget = new gp(); in main()
248 if(populationTarget->af == -1){ in main()
249 delete populationTarget; in main()
253 double ehet = 2*(populationTarget->af * (1 - populationTarget->af)); in main()
256 << populationTarget->af << "\t" in main()
258 << populationTarget->hfrq << "\t" in main()
259 << populationTarget->nhet << "\t" in main()
[all …]
H A DgenotypeSummary.cpp320 genotype * populationTarget ; in main() local
323 populationTarget = new pl(); in main()
326 populationTarget = new gl(); in main()
329 populationTarget = new gp(); in main()
332 populationTarget = new gt(); in main()
338 if(populationTarget->genoIndex[i] == -1){ in main()
341 else if (populationTarget->genoIndex[i] == 0) { in main()
348 else if (populationTarget->genoIndex[i] == 1){ in main()
351 else if (populationTarget->genoIndex[i] == 2) { in main()
360 cerr << populationTarget->genoIndex[i] << endl; in main()
[all …]
H A DvcfToHap.cpp388 genotype * populationTarget ; in main() local
391 populationTarget = new pl(); in main()
394 populationTarget = new gl(); in main()
397 populationTarget = new gp(); in main()
400 populationTarget = new gt(); in main()
405 if(populationTarget->af <= globalOpts.af || populationTarget->af >= (1-globalOpts.af) ){ in main()
406 delete populationTarget; in main()
410 afs.push_back(populationTarget->af); in main()
411 loadPhased(haplotypes, populationTarget, populationTarget->gts.size()); in main()
413 populationTarget = NULL; in main()
[all …]
H A DiHS.cpp607 genotype * populationTarget ; in main() local
610 populationTarget = new pl(); in main()
613 populationTarget = new gl(); in main()
616 populationTarget = new gp(); in main()
619 populationTarget = new gt(); in main()
625 || populationTarget->nref < 2 in main()
626 || populationTarget->nalt < 2){ in main()
627 delete populationTarget; in main()
632 loadPhased(haplotypes, populationTarget, populationTarget->gts.size()); in main()
634 populationTarget = NULL; in main()
[all …]
H A DmeltEHH.cpp592 genotype * populationTarget ; in main() local
595 populationTarget = new pl(); in main()
598 populationTarget = new gl(); in main()
601 populationTarget = new gp(); in main()
604 populationTarget = new gt(); in main()
610 || populationTarget->nref < 2 in main()
611 || populationTarget->nalt < 2){ in main()
612 delete populationTarget; in main()
617 loadPhased(haplotypes, populationTarget, populationTarget->gts.size()); in main()
619 populationTarget = NULL; in main()
[all …]
H A DplotHaps.cpp346 genotype * populationTarget ; in main() local
349 populationTarget = new pl(); in main()
352 populationTarget = new gl(); in main()
355 populationTarget = new gp(); in main()
358 populationTarget = new gt(); in main()
361 populationTarget->loadPop(target, var.sequenceName, var.position); in main()
364 afs.push_back(populationTarget->af); in main()
365 loadPhased(haplotypes, populationTarget, populationTarget->gts.size()); in main()

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