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@jeromekelleher jeromekelleher released this 20 Jun 13:05
0.1.2
9be1841
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Learn about vigilant mode.

Minor update to take advantage of msprime 0.6.0's Population and Individual objects and fix various bugs.

Breaking changes:

  • Bumped SampleData file format version to 1.0 because of the addition of individuals and populations. Older SampleData files will not be readable and must be regenerated.

  • Changed the order of the alleles and genotypes arguments to SampleData.add_site.

New features:

  • Sample and individual metadata now handled correctly.

  • Added --no-simplify option to CLI and simplify=True option to infer function.

  • Better handling of missing files (raises correct exceptions).

  • tsinfer list now presents basic information for .trees files.

Bug fixes:

  • Degenerate examples with zero inference sites are now rooted (#44)

  • Simplify=False results in tree sequence with correct sample nodes.

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