Isaac Overcast

I mean, I guess I haven't really needed it in more than a year, so...... Still it seemed like it was useful at one point, but now I just tell...

The goal of mindepth is to help identify sequencing error, if i understand correctly. If illumina error rate is < 0.1% I guess the question is, what are the chances...

Here's a [good tutorial for memory_profiler](https://www.huyng.com/posts/python-performance-analysis), as well as some other performance analysis stuff.

Hello, thank you for pointing this out and for giving such a detailed bug report. The 'decode' error is an old py2.7/py3 compatibility issue, and yes the fix that you...

Hm, well it looks like this would only ever happen if the number of loci that is being processed is zero. Can you show me the cell where you create...

Yes, well you can see here this is exactly what's happening: ``` [locus filter] full data: 130690 [locus filter] post filter: 0 ``` You have 0 loci that are shared...

I have not been able to reproduce this for either SE RAD or PE ddRAD on real data. @StuntsPT Can you dropbox me the hdf5 file? Or better a chunk...

__tldr;__: Yes the genotype counts are wrong in the vcf file, but the genotypes themselves are correct. Heterozygous sites ARE correct even if the counts are wrong. Got good news...

The "bad" individual has the incorrect genotype counts (" [66, 0, 0, 0]") in the neighborhood of the bad base: ``` >>> io5["catgs"][37200][16][30:40] array([[ 0, 66, 0, 0], [ 0,...

Also __NB:__ the actual cluster number for this locus inside the clust.hdf5 file is __37200__, and not `18106` as reported in the .loci file, this took me a while to...