This PR fixes the optional features build failures that we've been seeing in the past week by skipping the variant analysis script for rRNA gene RNAP densities if the IDs of the rRNAs listed in the dictionary do not match the IDs in sim_data. The analysis script was leading to failures in the no-operon runs of the optional features build and this fix will ensure that this analysis script is skipped for those runs. This PR also removes the assert statement in the ChromosomeStructure process that was triggering errors in some of @rjuenemann's runs. This statement was being triggered whenever there are RNAPs that are removed by collisions with replication forks that have not advanced at all from their starting locations. I did not think it would be worth the effort to have this statement handle this exception, especially since the statement was already checking something that was relatively trivial (despite this very rare exception).
This PR fixes the optional features build failures that we've been seeing in the past week by skipping the
variantanalysis script for rRNA gene RNAP densities if the IDs of the rRNAs listed in the dictionary do not match the IDs insim_data. The analysis script was leading to failures in the no-operon runs of the optional features build and this fix will ensure that this analysis script is skipped for those runs. This PR also removes theassertstatement in theChromosomeStructureprocess that was triggering errors in some of @rjuenemann's runs. This statement was being triggered whenever there are RNAPs that are removed by collisions with replication forks that have not advanced at all from their starting locations. I did not think it would be worth the effort to have this statement handle this exception, especially since the statement was already checking something that was relatively trivial (despite this very rare exception).