Scoary

- Bug fixes to vcf2scoary

- Apparently 1.6.14 did not fix the pip issue for all users. Deleted the function that seemed to cause the pip crash

- Fixed a bug where Scoary could not be upgraded using pip

- 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

- 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

- 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