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4 | 4 |
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5 | 5 | **Breaking Changes** |
6 | 6 |
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7 | | -- `TreeSequence.tables` now returns a zero-copy immutable view of the tables. |
8 | | - To get a mutable copy, use `TreeSequence.dump_tables()`. |
| 7 | +- ``TreeSequence.tables`` now returns a zero-copy immutable view of the tables. |
| 8 | + To get a mutable copy, use ``TreeSequence.dump_tables()``. |
9 | 9 | (:user:`benjeffery`, :pr:`3288`, :issue:`760`) |
10 | 10 |
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11 | | -- For a tree seqeunce to be valid mutation parents in the table collection |
| 11 | +- For a tree sequence to be valid mutation parents in the table collection |
12 | 12 | must be correct and consistent with the topology of the tree at each mutation site. |
13 | 13 | ``TableCollection.tree_sequence()`` will raise a ``_tskit.LibraryError`` if this |
14 | 14 | is not the case. |
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52 | 52 |
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53 | 53 | **Bugfixes** |
54 | 54 |
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55 | | -- In some tables with mutations out-of-order `TableCollection.sort` did not re-order |
56 | | - the mutations so they formed a valid TreeSequence. `TableCollection.sort` and |
57 | | - `TableCollection.canonicalise` now sort mutations by site, then time (if known), |
| 55 | +- In some tables with mutations out-of-order ``TableCollection.sort`` did not re-order |
| 56 | + the mutations so they formed a valid TreeSequence. ``TableCollection.sort`` and |
| 57 | + ``TableCollection.canonicalise`` now sort mutations by site, then time (if known), |
58 | 58 | then the mutation's node's time, then number of descendant mutations |
59 | 59 | (ensuring that parent mutations occur before children), then node, then |
60 | 60 | their original order in the tables. (:user:`benjeffery`, :pr:`3257`, :issue:`3253`) |
|
68 | 68 | (:user:`benjeffery`, :pr:`3246`, :issue:`3244`) |
69 | 69 |
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70 | 70 | - k-way statistics no longer require k sample sets, allowing in particular |
71 | | - "self" comparisons for `TreeSequence.genetic_relatedness`. This changes the |
| 71 | + "self" comparisons for ``TreeSequence.genetic_relatedness``. This changes the |
72 | 72 | error code returned in some situations. |
73 | 73 | (:user:`andrewkern`, :user:`petrelharp`, :pr:`3235`, :issue:`3055`) |
74 | 74 |
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|
107 | 107 | - Add ``TreeSequence.map_to_vcf_model`` method to return a mapping of |
108 | 108 | the tree sequence to the VCF model. |
109 | 109 | (:user:`benjeffery`, :pr:`3163`) |
| 110 | + |
110 | 111 | - Use a thin space as the thousands separator in HTML output, |
111 | 112 | and a comma in CLI output. |
112 | 113 | (:user:`hossam26644`, :pr:`3167`, :issue:`2951`) |
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