Python 0.6.4

Breaking changes

• TreeSequence.write_vcf now filters non-sample nodes from individuals
  by default, instead of raising an error. These nodes can be included using the
  new include_non_sample_nodes argument.
  By default individual names (sample IDs) in VCF output are now of the form
  tsk_{individual.id} Previously these were always
  "tsk_{j}" for j in range(num_individuals). This may break some downstream
  code if individuals are specified. To fix, manually specify individual_names
  to the required pattern.
  (@benjeffery, #3163)

Features

• Add TreeSequence.sample_nodes_by_ploidy method to return the sample nodes
  in a tree sequence, grouped by a ploidy value.
  (@benjeffery, #3157)

• Add TreeSequence.individuals_nodes attribute to return the nodes
  associated with each individual as a numpy array.
  (@benjeffery, #3153)

• Add shift method to both TableCollection and TreeSequence classes
  allowing the coordinate system to be shifted, and TreeSequence.concatenate
  so a set of tree sequence can be added to the right of an existing one.
  (@hyanwong, #3165, #3164)

• Add TreeSequence.map_to_vcf_model method to return a mapping of
  the tree sequence to the VCF model.
  (@benjeffery, #3163)

• Use a thin space as the thousands separator in HTML output,
  and a comma in CLI output.
  (@hossam26644, #3167, #2951)

Fixes

• Correct assertion message when tables are compared with metadata ignored.
  (@benjeffery, #3162, #3161)