v1.6.16 (Aug 2017)
- Bug fixes to vcf2scoary
v1.6.15 (Jul 2017)
- Deleted a function that would prevent scoary from being installed through pip for some users
v1.6.13 (Jul 2017)
- Fixed a bug where Scoary would not handle converted VCF files due to different headers
- Changed the parameters of --test
- Fixed the GUI that was broken since 1.6.12 due to introduction of --include_input_columns
- Include_input_columns now correctly handles the ALL keyword
- Added the ExampleVCFTrait.csv file to test VCF functionality
v1.6.12 (Jun 2017)
- Convert VCF files to Roary/Scoary format, allowing analysis on a wide range of variants (SNPs, indels, structural variations etc)
- Grab columns from the Roary input and put in the output (To get strain-specific protein names, for example)
- Scoary now comes with a manual, located under docs/tex/scoary_manual.pdf
- The log now includes the original command line
v1.6.11 (Apr 2017)
- Blank values in trait files will now correctly be read as missing. Fixes (#54)
- Added --no_pairwise option for simple set differences / categorical enrichment analysis without causal hypothesis (As requested among others in (#53)
- Modified GUI with no_pairwise and slightly modified look.
- Added ExampleTree.nwk to exampledata
- Added support for travis. (CI tests will be further developed)
- Added example cases in README.md
- Fixed broken links in README.md
v1.6.10 (Jan 2017)
- Scoary now creates a log file (both in terminal and GUI mode)
- Fixed a bug where empirical p-values would exceed 1.0
- Fixed a bug where Scoary would crash when pruning many isolates from the internally calculated phylogenetic tree
v1.6.9 (Dec 2016)
- Scoary now handles missing data specified in the traits file as "NA", "-" or ".".
- Now also handles missing isolates (rows) in the traits file.
- Stylistic changes, including line lengths formats to conform with PEP8.
v1.6.8 (29th Nov 2016)
- Bugfix: Addition of numpy.float64 and long were causing problems on some systems. Now converted to float beforehand. (Fixes #43)
v1.6.7 (28th Nov 2016)
- Scoary article is now out! Updated Readme and citation.