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original.CopyParameters(mp);
original.CopyParameters(mp);
// =======================================================================================
// We can update parameters by comparing a reference haplotype to the others =============
#pragma omp parallel for
#pragma omp parallel for
for (int i = 0; i < iterations; i++)
for (int i = 0; i < iterations; i++)
}
}
// =======================================================================================
// Or, by comparing a sampled haplotype to the reference =================================
if (round >= rounds / 2)
if (round >= rounds / 2)
{
{
}
}
}
}
// =======================================================================================
// At the end of each iteration, we need to update the model =============================
mp.UpdateModel();
mp.UpdateModel();
}
}
reference.ListMajorAlleles();
reference.ListMajorAlleles();
// =======================================================================================
// Now, we can do some imputation - but first open output files! =========================
// Output some basic information
printf("Imputing Genotypes ...\n");
printf("Imputing Genotypes ...\n");
ImputationStatistics stats(reference.markerCount);
ImputationStatistics stats(reference.markerCount);
// Impute each haplotype
// =======================================================================================
// Now, loop through haplotypes, imputing one at a time ==================================
#pragma omp parallel for
#pragma omp parallel for
for (int i = 0; i < target.count; i++)
for (int i = 0; i < target.count; i++)
}
}
// ============================================================================
// Close output files =========================================================
ifclose(dosages);
ifclose(dosages);
if (probabilities != NULL)
if (probabilities != NULL)
ifclose(probabilities);
ifclose(probabilities);
// ===========================================================================
// Report runtime statistics =================================================
time_t stop = time(NULL);
time_t stop = time(NULL);
