This PR fixes a bug that was leading to some simulations being initialized with the wrong chromosome state when the mechanistic_replisome option is turned off, which is the default setting for our simulations currently. During initialization, we were limiting the number of starting replication forks based on how many replisome subunits exist at initialization, which is the correct behavior only if this option is on. I added some simple if-else statements to check this option and change how we initialize replication forks accordingly.
This PR fixes a bug that was leading to some simulations being initialized with the wrong chromosome state when the
mechanistic_replisomeoption is turned off, which is the default setting for our simulations currently. During initialization, we were limiting the number of starting replication forks based on how many replisome subunits exist at initialization, which is the correct behavior only if this option is on. I added some simple if-else statements to check this option and change how we initialize replication forks accordingly.