Hi All,
I'm pleased to release Stacks version 2.3 today -- really the icing on
the cake of the version 2 code base. Lots of nice, small changes to
improve various aspects of performance.
http://catchenlab.life.illinois.edu/stacks
Stacks 2.3 - Jan 11, 2019
--------------------------
Feature: populations: Backwards-compatibly worked on filtering options;
added long names for -r and -p and added --min-samples-overall
and --filter-haplotype-wise.
Feature: populations: Implemented --treemix.
Feature: gstacks: Improved RAD-loci reference sequences around the end
of forward (restriction site-bound) reads.
Feature: gstacks: Improved the way 2-microsatelittes are dealt with.
Feature: gstacks: Changed the default value for --var-alpha from 0.05 to
0.01 (--gt-alpha is unchanged at 0.05).
Feature: gstacks: Improved PCR duplicates-related log information
(distribution of clone sizes).
Feature: gstacks: Added an option to save read alignments
(--write-alignments) to BAM files.
Feature: Backwards-compatibly switched to hyphens in command line
options (underscores remain accepted where they previously
were).
Feature: cstacks/sstacks now report an error when the disk becomes full.
Best,
julian