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standage
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Dec 7, 2019
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| - `ID`: a unique identifier for this population across all sources | ||
| - `Name`: a free-text description of the population, intended to be human readable | ||
| - `Xref`: optional cross-reference |
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The Xref column was added back as a requirement for population tables.
standage
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This update makes sweeping changes to the genotype simulation and sequencing code. - The `sim` module no longer performs sequencing and focuses entirely on haplotype simulation. - The `seq` module now handles simulated Illumina sequencing of both simple (single contributor) and mixture (multi contributor) samples. - The `mix` module merges simple genotypes into a simulated mixture sample. - The `mixture` module has been dropped, and its functionality is covered by the more granular `sim`, `mix`, and `seq` modules. This update also replaced all references to `microhapulator.cli.parse_args()` with `microhapulator.cli.get_parser().parse_args()`. The former is used to configure runtime logging, which for some reason causes issues in a testing environment. Closes #44.
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Sep 11, 2024
Oops. These changes were supposed to be part of #45.
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While preparing for #42, I discovered that the 26 global populations from the 1000 Genomes Project are included in the 96 ALFRED populations, under different IDs. This update adds a new data source to the
dbbuilddirectory, and the 26 1KGP population definitions were moved fromdbbuild/sources/alfred/todbbuild/sources/1kgp/. At the moment, themarker.tsvandfrequency.tsvfiles indbbuild/sources/1kgpare empty, but frequency data will be added as part of #42.Closes #44.