diff --git a/CHANGELOG.md b/CHANGELOG.md index 1d2a05cf..39e48616 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,27 +1,47 @@ # Changelog -## [0.2.4] - 2022-06-xx +## [0.3] - 2022-06-xx **Features** +- When calling `sample_data.add_site()` the ancestral state does not need to be the + first allele (index 0): alternatively, an ancestral allele index can be given + (and if `MISSING_DATA`, the ancestral state will be imputed). ({pr}`718`, + {issue}`686` {user}`hyanwong`) + +- The CLI interface now allows recombination rate (or rate maps) and mismatch ratios + to be specified ({pr}`731`, {issue}`435` {user}`hyanwong`) + +- The calls to match-ancestors and match-samples via the CLI are now logged + in the provenance entries of the output tree sequence ({pr}`732` and `741`, + {issue}`730` {user}`hyanwong`) + +- The CLI interface allows `--no-post-process` to be specified (for details of post- + processing, see "Breaking changes" below) ({pr}`727`, {issue}`721` {user}`hyanwong`) + - matching routines warn if no inference sites ({pr}`685`, {issue}`683` {user}`hyanwong`) **Fixes** -- sample_data.subset() now accepts a sequence_length ({pr}`681`, {user}`hyanwong`) +- `sample_data.subset()` now accepts a sequence_length ({pr}`681`, {user}`hyanwong`) -- `verify` no longer raises error when comparing a genotype to missingness. ({pr}`716`, {issue}`625`, {user}`benjeffery`) +- `verify` no longer raises error when comparing a genotype to missingness. + ({pr}`716`, {issue}`625`, {user}`benjeffery`) **Breaking changes**: -- The ``simplify`` parameter is now deprecated in favour of ``post_process``, which +- The `simplify` parameter is now deprecated in favour of `post_process`, which prior to simplification, removes the "virtual-root-like" ancestor (inserted by tsinfer to aid the matching process) then splits the grand MRCA into separate pieces. - If splitting is not required, the ``post_process`` step can also be called as a - separate function with the parameter ``split_mrca=False`` (:pr:`687`, - :issue:`673`, :user:`hyanwong`) + If splitting is not required, the `post_process` step can also be called as a + separate function with the parameter `split_mrca=False` ({pr}`687`, + {issue}`673`, {user}`hyanwong`) +- Post-processing by default erases tree topology that exists before the first site + and one unit after the last site, to avoid extrapolating into regions with no data. + This can be disabled by calling `post_process` step as a separate function with the + parameter `erase_flanks=False` ({pr}`720`, {issue}`483`, {user}`hyanwong`) - Inference now sets time_units on both ancestor and final tree sequences to tskit.TIME_UNITS_UNCALIBRATED, stopping accidental use of branch length