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CLI returning haploid samples, API diploid #1451
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a little bit more info here.. Doing a dry run from the API indicates that contig ploidy is not the issue: Contig Description:
Contig origin: chr1:0-3042767
Contig length: 3042767.0
Contig ploidy: 2
Mean recombination rate: 8.064516129032259e-10
Mean mutation rate: 7.1e-09
Genetic map: None |
Can you give us the output of |
I see what's happening here: @andrewkern, you're using the deprecated API for sample specification, which is haploid for back compatibility. If instead, you run:
|
We may want to print a warning regarding ploidy, if the deprecated API is used? Currently, the warning that is printed is:
|
nice catch @nspope. beyond updating the warning, we're going to have to update the workshop notebooks (i'll volunteer given that I just ran a workshop), and probably should change the documentation. currently we say this about the |
Andy updated the notebooks already; it looks like the warning needs updating still. |
In comparing output from the API and the CLI during the probgen workshop I noticed a discrepancy in the ploidy output through a conversion to vcf. I think the issue is on the CLI side.
Here's an example. First using the CLI
notice the ploidy above
I can compare this to output from the API
then let's look at the vcf output from the API
diploid, as I would have expected.
I'm guessing this has to do with the assignment of ploidy through the CLI. Could it be that contigs have the wrong ploidy here?
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