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;
}
