release v2.3

[Catchen, Julian]

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

[Nicolas Rochette]

Hi all,

Since releasing version 2.3 ten days ago, we have become aware of limit
cases that confused gstacks program and caused it to conservatively
abort. Thank you to those who have reported these behaviors.

We have now released a patched version, version 2.3b, that fixes the
handling of these cases and restores the usual stability. Note that, if
you have used version 2.3 on your data and it did not crash, the results
are safe to use as they are. The results obtained with v2.3b will be
identical for most cases and very similar for a tiny minority of cases.

http://catchenlab.life.illinois.edu/stacks

Stacks 2.3b - Jan 23, 2019
----------
Bugfix: Fixed some limit cases causing an abort at gstacks.cc:1752.
Bugfix: Fixed some limit cases causing an abort at debruijn.cc:60.
Bugfix: Fixed some limit cases apparently causing an infinite loop in
the de Bruijn code.
Bugfix: Restored compilation with the oldest C++11 GCC versions (4.9 and
5.0).

Best,

Nicolas