These are chat archives for dereneaton/ipyrad

Oct 2016
Deren Eaton
Oct 06 2016 01:42
thanks @edgardomortiz , you were no the right track. Its working now for the next update.
Deren Eaton
Oct 06 2016 21:56

v.0.4.2 is now available. Lots of bug fixes and new features:
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 (0,0,0,0).
  • 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
  • Added -t option to allow fine-tune setting of threaded binaries (defaults to 2).

Bug Fixes:

  • 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.