This PR makes changes to the synth_prob_from_ppgpp function that we use to calculate ppGpp-adjusted synthesis probabilities for each gene. Before the change, this function used the replication_coordinate value in rna_data to normalize the calculated synthesis probabilities by the expected average copy number of the gene. This was problematic for variants where the replication_coordinate value was adjusted for some of the genes, because the pre-normalized synthesis probabilities are calculated by the ParCa using the pre-variant wildtype coordinates, while in this function the values in replication_coordinate are the values adjusted by the variant. With the changes, we have another column in the rna_data struct array that saves the wildtype coordinates, which the synth_prob_from_ppgpp function now uses to calculate per-copy synthesis probabilities.
This PR makes changes to the
synth_prob_from_ppgppfunction that we use to calculate ppGpp-adjusted synthesis probabilities for each gene. Before the change, this function used thereplication_coordinatevalue inrna_datato normalize the calculated synthesis probabilities by the expected average copy number of the gene. This was problematic for variants where thereplication_coordinatevalue was adjusted for some of the genes, because the pre-normalized synthesis probabilities are calculated by the ParCa using the pre-variant wildtype coordinates, while in this function the values inreplication_coordinateare the values adjusted by the variant. With the changes, we have another column in therna_datastruct array that saves the wildtype coordinates, which thesynth_prob_from_ppgppfunction now uses to calculate per-copy synthesis probabilities.