genomicSimulationC v0.2.4.003

Bug Fixes

• Group modification functions (split_ prefix) no longer fail if there are more than 10 groups in existence.

Improvements

• Significant under-the-hood changes to split_-prefixed functions. They now use BidirectionalIterator and RandomAccessIterator to find members of the group to split, and some call _split-prefixed generic functions to reduce code duplication.
• split_-prefixed functions now return the number of groups they created, rather than being void functions. Thanks to the GroupNum type (introduced v0.2.4) we can avoid confusion over whether the return value of these functions represents a group identifier or a count of groups.
  • For users, this will mean it is no longer necessary to zero the output array passed to these functions so that you can identify how many entries are the newly-created groups after the function finishes execution. Instead, the return value lets you know how many entries have been saved to the output array.
• BREAKING CHANGE: split_into_families and split_into_halfsib_families now take a parameter for length of the output array, and will truncate output if they find more families than that.
• Added a cache n_groups inside SimData to track the number of groups present in simulation at the current point in time. This allows users to know how much space to allocate before calling functions like get_existing_groups and get_existing_group_counts, and the program to know how much space to allocate inside split_into_families and split_into_halfsib_families. This will help avoid issues around truncated output or memory overruns.
  • Specifically, this cache is an upper bound on the number of groups currently present in simulation, because split_from_group is not aware if it has destroyed a group by moving the entire group into its new one.
  • get_existing_groups and get_existing_group_counts will update n_groups to the true value of the number of groups in simulation as a side-effect of their calls.
• BREAKING CHANGE: Function signatures of get_existing_groups and get_existing_group_counts are slightly different. They can now be passed NULL to output parameters that you don't need, and they assume that their not-NULL output parameters are of length SimData.n_groups at least, rather than asking for the length of their output parameters separately.
• Gradual transformation of genotype indexes from unsigned int type to a size_t type. This conversion is now implemented in the iterators and get_group_indexes.
• New iterator helper function set_group, to go alongside get_group, get_id, etc. It is currently the only iterator helper function that modifies data.
• BidirectionalIterators now use local position rather than global position. Just in case of hypothetical really huge simulations.
• Removed some qsort comparator functions that are no longer called by anything.