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Revision as of 15:06, 13 September 2013
, 15:06, 13 September 2013Created page with "</source lang="cpp"> void Haplotyper::ImputeGenotypes() { RewindMemoryPool(); // Process the last position RetrieveMemoryBlock(markers - 1); ImputeGenotypes(le..."
</source lang="cpp">
void Haplotyper::ImputeGenotypes()
{
RewindMemoryPool();
// Process the last position
RetrieveMemoryBlock(markers - 1);
ImputeGenotypes(leftMatrices[markers - 1], markers - 1);
SetupPrior(rightMatrices[0]);
ConditionOnData(rightMatrices[0], 0, current_genotypes[0]);
float *temp;
float *from = rightMatrices[0];
float *to = rightMatrices[1];
for (int i = markers - 2; i >= 0; i--)
{
// Move things along
Transpose(from, to, thetas[i]);
// Find nearest informative marker
double theta = 0.0;
int left = i;
while (left > 0 && genotypes[states / 2][left] == GENOTYPE_MISSING)
{
// Cumulative recombination fraction to nearest marker
theta = theta + thetas[left - 1] - theta * thetas[left - 1];
left--;
}
RetrieveMemoryBlock(left);
float * leftMatrix = leftMatrices[left];
if (left != i)
{
Transpose(leftMatrix, from, theta);
leftMatrix = from;
}
ImputeGenotypes(leftMatrix, to, i);
ConditionOnData(to, i, genotypes[states / 2][i]);
temp = from;
from = to;
to = temp;
}
}
</source>
void Haplotyper::ImputeGenotypes()
{
RewindMemoryPool();
// Process the last position
RetrieveMemoryBlock(markers - 1);
ImputeGenotypes(leftMatrices[markers - 1], markers - 1);
SetupPrior(rightMatrices[0]);
ConditionOnData(rightMatrices[0], 0, current_genotypes[0]);
float *temp;
float *from = rightMatrices[0];
float *to = rightMatrices[1];
for (int i = markers - 2; i >= 0; i--)
{
// Move things along
Transpose(from, to, thetas[i]);
// Find nearest informative marker
double theta = 0.0;
int left = i;
while (left > 0 && genotypes[states / 2][left] == GENOTYPE_MISSING)
{
// Cumulative recombination fraction to nearest marker
theta = theta + thetas[left - 1] - theta * thetas[left - 1];
left--;
}
RetrieveMemoryBlock(left);
float * leftMatrix = leftMatrices[left];
if (left != i)
{
Transpose(leftMatrix, from, theta);
leftMatrix = from;
}
ImputeGenotypes(leftMatrix, to, i);
ConditionOnData(to, i, genotypes[states / 2][i]);
temp = from;
from = to;
to = temp;
}
}
</source>
