pyrad issues

error when param 29 is empty or is 0,0 in pairddrad

Found issue in PyRAD 3.0.66 with the dataset: http://www.dereneaton.com/downloads/simpairddrads.zip Step 6 fails in pairddrad mode if ## 29.opt has an empty value or if the value is 0,0 I had...

charmichaeld

Fixing newline formatting in VCF

Currently, if the first locus in .loci does not contain a polymorphic site then the first line after the header is a blank line. Changed loci2vcf.py here in line 64...

atcg

Problem parsing new .loci format

I'm not sure if this fix is needed for other output formats, but this worked to fix issues I was seeing in VCF outputs.

jpuritz

How to install pyrad without root access?

2

HI, is there a way to install pyrad without root access? If yes, how to do it??

uloeber

error when param 28 is empty in pairddrad

dereneaton

allow minCov parameter to be a proportion

Currently you have to provide ## 12. minCov parameter in the input file as the minimum number of individuals. Allowing this to be a proportion, similar to ## 13. maxSharedH...

TomaszSuchan

I have created a conda package for pyrad that pulls in ALL deps (muscle and vsearch too)

3

Because I generally work on multiple clusters, I have to replicate my scientific software stack not infrequently and I generally hate my life for a few days each time I...

xguse