Isaac Overcast
Isaac Overcast
There's a way to get the (properly formatted) API to automatically generate for the rtfd docs, it's really useful. I've done it for MESS and it's not that hard, and...
It seems at the moment that invoking ipyrad with the `--ipcluster` flag works great, but then it looks like it kills the engines and stops ipcluster after it finishes running....
The [structure file format](https://www.ccg.unam.mx/~vinuesa/tlem09/docs/structure_doc.pdf) supports an optional 2nd column to indicate (with integer values) the a priori population from which each sample was obtained (e.g. sampling site). In ipyrad if...
Looks like [fastq-dump will be deprecated](https://hpc.nih.gov/apps/sratoolkit.html), and the replacement (fasterq-dump) is better, so we should swap out or at least test for fasterq-dump _first_ and then maybe fall back to...
Over the past couple days I've gotten pretty handy with scikit-allel, a nice python package for generating simple popgen summary stats. I think it would be relatively straightforward to include...
This was useful, and was blanked in v.0.9. The -d flag literally was doing nothing for the CLI except making it so you had to run the failed command twice...
Toytree 0.2 api breaks bpp and tetrad analysis tools. Need to update to reflect the new API. FOr now rolling back to toytree=0.1.27 fixes the problem, but should fix the...
When filtering the unlinked snps files it would be useful to have a parameter to control how sites with indels are treated. Maybe the filter can just ignore all indel...
Right now the default imputation scheme converts missing data into ancestral alleles, which creates a strong affinity among samples with lots of missingness. What if instead of this, missing data...
Somebody in gitter reported trim_loci wasn't working for the distal end of R1 and i checked and it is true that it's not doing anything. In debugging this I see...