void CrossHypotheses::FillInPrediction(PersistingThreadObjects &thread_objects, ExtendedReadInfo &my_read, InputStructures &global_context) {
// Check validity of input arguments
if (my_read.start_flow < 0 or my_read.start_flow >= global_context.treePhaserFlowOrder.num_flows()) {
cerr << "CrossHypotheses::FillInPrediction: Start flow needs to be be larger than zero and smaller than the number of flows." << endl;
cerr << "Start flow: " << my_read.start_flow << " Number of flows: " << global_context.treePhaserFlowOrder.num_flows();
assert(my_read.start_flow >= 0 and my_read.start_flow < global_context.treePhaserFlowOrder.num_flows());
}
if (my_read.phase_params.size() != 3) {
cerr << "CrossHypotheses::FillInPrediction: There need to be 3 phase parameters!" << endl;
assert(my_read.phase_params.size() != 3);
}
for (int i=0; i<3; i++) {
if (my_read.phase_params[i] < 0 or my_read.phase_params[i] > 1) {
cerr << "CrossHypotheses::FillInPrediction: Phase parameters should be positive and smaller than one!" << endl;
assert(my_read.phase_params[i] >= 0 and my_read.phase_params[i] <= 1);
}
}
// allocate everything here
CleanAllocate(instance_of_read_by_state.size(), global_context.treePhaserFlowOrder.num_flows());
max_last_flow = CalculateHypPredictions(thread_objects, my_read, global_context,
instance_of_read_by_state, predictions, normalized);
SetModPredictions();
if (my_read.alignment.AlignmentFlag>0)
strand_key = 1;
else
strand_key = 0;
}
void CrossHypotheses::FillInPrediction(PersistingThreadObjects &thread_objects, const Alignment& my_read, const InputStructures &global_context) {
// allocate everything here
CleanAllocate(instance_of_read_by_state.size(), global_context.treePhaserFlowOrder.num_flows());
int flow_upper_bound = splice_end_flow + 4*min_delta_for_flow;
max_last_flow = CalculateHypPredictions(thread_objects, my_read, global_context,
instance_of_read_by_state, predictions, normalized, flow_upper_bound);
SetModPredictions();
if (my_read.is_reverse_strand)
strand_key = 1;
else
strand_key = 0;
}
void CrossHypotheses::FillInPrediction(PersistingThreadObjects &thread_objects, const Alignment& my_read, const InputStructures &global_context) {
// allocate everything here
CleanAllocate(instance_of_read_by_state.size(), global_context.flow_order_vector.at(my_read.flow_order_index).num_flows());
// We search for test flows in the flow interval [(splice_start_flow-3*max_flows_to_test), (splice_end_flow+4*max_flows_to_test)]
// We need to simulate further than the end of the search interval to get good predicted values within
int flow_upper_bound = splice_end_flow + 4*max_flows_to_test + 20;
max_last_flow = CalculateHypPredictions(thread_objects, my_read, global_context, instance_of_read_by_state,
same_as_null_hypothesis, predictions_all_flows, normalized_all_flows, flow_upper_bound);
SetModPredictions();
if (my_read.is_reverse_strand)
strand_key = 1;
else
strand_key = 0;
}
void CrossHypotheses::InitializeDerivedQualities() {
InitializeResponsibility(); // depends on hypotheses
// in theory don't need to compute any but test flows
SetModPredictions(); // make sure that mod-predictions=predictions
ComputeBasicResiduals(); // predicted and measured
InitializeSigma(); // depends on predicted
my_t.SetV(heavy_tailed);
ComputeBasicLikelihoods(); // depends on residuals and sigma
// compute log-likelihoods
ComputeLogLikelihoods(); // depends on test flow(s)
}