C API C_1.2.0

Breaking changes

• Remove tsk_diff_iter_t and associated functions.
  (@benjeffery, #3221, #2797).

• tsk_treeseq_init now requires that mutation parents in the table collection
  are correct and consistent with the topology of the tree at each mutation site.
  Returns TSK_ERR_BAD_MUTATION_PARENT if this is not the case, or
  TSK_ERR_MUTATION_PARENT_AFTER_CHILD if the mutations are not in an order
  compatible with the correct mutation parent.
  (@benjeffery, #2729, #2732, #3212).

Features

• Add TSK_TS_INIT_COMPUTE_MUTATION_PARENTS to tsk_treeseq_init
  to compute mutation parents from the tree sequence topology.
  Note that the mutations must be in the correct order.
  (@benjeffery, #2757, #3212).

• Add TSK_CHECK_MUTATION_PARENTS option to tsk_table_collection_check_integrity
  to check that mutation parents are consistent with the tree sequence topology.
  This option implies TSK_CHECK_TREES.
  (@benjeffery, #2729, #2732, #3212).

• Add the TSK_NO_CHECK_INTEGRITY option to tsk_table_collection_compute_mutation_parents
  to skip the integrity checks that are normally run when computing mutation parents.
  This is useful for speeding up the computation of mutation parents when the
  tree sequence is certainly known to be valid.
  (@benjeffery, #3212).

• Mutations returned by tsk_treeseq_get_mutation now include pre-computed
  inherited_state and inherited_state_length fields. The inherited state
  is computed during tree sequence initialization and represents the state that
  existed at the site before each mutation occurred (either the ancestral state
  if the mutation is the root mutation or the derived state of the parent mutation).
  Note that this breaks ABI compatibility due to the addition of these fields
  to the tsk_mutation_t struct.
  (@benjeffery, #3277, #2631).