v.0.4.2 is now available. Lots of bug fixes and new features:
trim_overhang now defaults to trimming edges to
min(4, minsamp), and then trims additionally the number of bases indicated by
trim_overhang. Default setting is therefore now
- Merging can now be done at any step.
- Samples can be designated to be dropped (as opposed to only being designated as kept) during branching by adding the "-" symbol, like this:
ipyrad -p params-test.txt -b new - sample1 sample2
- Added more warnings and error messages
- faster step6
- prettier progress printing in CLI and especially to API
- Parallelized sorted fastq loading in step 1
-t option to allow fine-tune setting of threaded binaries (defaults to 2).
- Fixed overzealous warning message in demultiplexing when allowing base mismatches
- Header was not printing in vcf files
- step1 would not kill
- Fix for merging Samples when merged Assemblies have Samples with the same names.