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Here's a (very!) rough first pass at an illustrative figure 1. The idea is to have a number of panels showing different aspects of the software:
a. Show the catalogue in a tree-like way. We want to…
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The tutorial and catalog section contain examples that are now out of date.
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Running `python -m jcvi.assembly.allmaps merge ` on my own maps (a male and female linkage map, formated identically to the CSV files in the example) resulted in a collision of map names...See outpu…
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As discussed in meeting May 7th. Are you leading this one @andrewkern?
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after reading through all the relevant bits of docs/help and the `get_contig` API, I'm still a little confused about how the `length-multiplier` option is actually changing the simulation. If I specif…
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ref #1265 - this needs a dedicated discussion
From @amsnyder210:
> Currently, "geography" for Arctos records is political (state, county, country, etc). Enabling users to query drainages in *hig…
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@daniel-goldstein and I are investigating if msprime can be updated to run simulations directly in physical space rather than simulating in genetic space as we currently do. The advantage of working d…
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I've been trying to run the Arabidopsis model with the snakemake pipeline and have been getting the error:
`UserWarning: Warning: recombination map not found for chromosome: 'chr5' on map: 'Salome2…
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PR #45 adds the ability to reproducibly run standard simulations from the command line, which is a real win in terms of usability. During the process of working through this change, it's become clear …
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I get an error when doing:
```
stdpopsim homsap -g HapmapII_GRCh37 -c chr22 -o foo.ts --model ooa_2 2 3
```
```
2019-11-29 10:43:38,515 [93420] CRITICAL root: Traceback (most recent call last)…