1.2.0

Release notes:

• Introduced a parameter -f in the depth command to specify the minimum frequency of a marker in all individuals to retain this marker in depth computations (default value is 0.75, which was the value used before exposing this parameter)
• RADSex now checks that markers are retained when computing average and median depths with the depth command and exits with an error when no markers are retained

1.1.3

• Implemented latest BWA library to provide support for gcc >= 10
• Minor syntax changes to the code to compile on latest OSX version

1.1.2

Changelog:

• Fixed a bug in 'map' that occurred with low sample numbers (#18); group counts are now properly initialized to 0 for all groups in each marker when parsing the markers table.
• Internal: added a 'get_groups' method to Popmap that returns a list of all groups in the groups info file.

1.1.1

Fixed a bug with the number of individual in the output of freq

1.1.0

This release adds informative comment lines to the output of 'freq', 'distrib', and 'map' and improves comment lines for the output of 'signif' and 'subset' for consistency. Requires sgtr 1.1.0 to visualize results.

1.0.1

This release includes a small update to fix a bug with the comment and header lines in the tabulated output of "subset"

1.0.0

First official release of radsex.

Summary of changes from 0.2.0:

• Complete overhaul of the command line interface, not compatible with pre-1.0.0 versions. The new interface is designed to be consistent and convenient and should not change in the future.

• Groups to compare can now be specified with the --groups / -G parameter, allowing flexibility in group names in the popmap.

• Output files have changed; most output files have comment lines indicating the parameters used in the analysis that generated them. Output files contain more information than before.

• Updated "depth" command to compute statistics on marker depths.

• Internal: complete reorganization of radsex's code and documentation, should make updating radsex much easier in the future.

In parallel, radsex-vis was merged in the new R package sgtr. The radsex-vis repository will remain for legacy reasons but radsex-vis will not work with the output of radsex >= 1.0.0.

This release underwent a good amount of testing but there are most likely bugs remaining. If you encounter a bug, please open an issue! You can also use issues to suggest new features or updates to the RADSex workflow.

Version 0.2.0

This beta release brings the following changes:

• a new subcommand ("depth") to compute the number of retained reads for each individual.
• major documentation update

First round of bugfixes for Bioconda

v0.1.1

Removed unused demultiplexing code

First official beta RADSex release for Bioconda

This is the first official beta release of RADSex.
The software is usable and a basic documentation is available on readthedocs.
Bug fixes, new features, and performance improvements may come before the 1.0.0 release.
Parameter and function names are also subject to change until 1.0.0