Version 1.4.2 - Home laboratory

v1.4.2 (13th Sep 2016)

Fixed a bug that would cause Scoary to crash if ran without any -c options.

v1.4.1 (8th Sep 2016)

Fixed a bug where results in the output file did not have quotes around them. This could interfere with annotations that have delimiters (like commas) in them.

v1.4.0 (7th Sep 2016)

-The correction options are now a lot more sophisticated, and allow multiple restrictions with individual p-values to be set.
-Fixed a bug that would sometimes result in a too strict Bonferroni p-value in the results.
-No-time now also applies to the reduced gene presence/absence file.
-The results sorting now works a little differently. When using only pairwise comparisons filtering, results will be sorted by these p-values. When other filters (Individual, Bonferroni, Benjamini-Hochberg) are used, results will be sorted by these instead.
-Fixed a bug where the program would crash if you specified a very large max_hits.
-The citation option has been added, and includes a nifty ASCII logo.
-Some optimization when using pairwise comparison to filter results.

v1.3.7 (2nd Sep 2016)

-The no-time argument can now be used to avoid output files (results and tree file) to come with a timestamp in the name. Should make it easier to implement Scoary in automated pipelines. (Credits: Marco Galardini)
-Comma is now the default delimiter in input and output files. The user can specify another input/output delimiter with the delimiter argument. (Note that the two input files and the output files will all have the same delimiter)
-Bug fixes that caused python3 problems in 1.3.6 (Credits: Marco Galardini)

v1.3.6 (28th Jul 2016)

-Simulated example data is included in the exampledata folder. This is primarily intended as a guide to how input files can look, as well as giving users a quick view at what the program can do. Running Scoary with the --test flag will overrun all other options (except --version) and automatically run the exampledata with default options.