sample_t sample( gsl_rng * r,
const poptype & p,
const unsigned deme,
const unsigned nsam,
const bool removeFixed )
/*!
Take a random sample of nsam chromosomes from a meta-population
\param r A random-number generator
\param p A population
\param p the index of the deme to sample
\param nsam The sample size
\param removeFixed Whether or not to remove variants present in all nsam chromosomes
\return A vector of both neutral and non-neutral variants
*/
{
static_assert( std::is_same<typename poptype::popmodel_t,sugar::METAPOP_TAG>::value,
"METAPOP_TAG required");
if(deme >= p.diploids.size())
{
throw std::out_of_range("KTfwd::sample_separate: deme index out of range");
}
auto temp = ms_sample_separate(r,p.mutations,p.gametes,p.diploids[deme],nsam,removeFixed);
auto rv = std::move(temp.first);
std::move(temp.second.begin(),temp.second.end(),std::back_inserter(rv));
std::sort(rv.begin(),rv.end(),[](const sample_site_t & a,
const sample_site_t & b){
return a.first<b.first;
});
if(!removeFixed)
add_fixations(&rv,p.fixations,nsam,sugar::treat_neutral::ALL);
return rv;
}
void
finish_sample(sample_t &sample, const vec_mutation_t &fixations,
const unsigned nsam, const bool removeFixed,
const sugar::treat_neutral treat)
{
if (!removeFixed)
{
add_fixations(sample, fixations, nsam, treat);
}
std::sort(sample.begin(), sample.end(),
[](const sample_site_t &a, const sample_site_t &b) noexcept {
return a.first < b.first;
});
if (!removeFixed)
{
sample.erase(std::unique(sample.begin(), sample.end()),
sample.end());
}
}