Update README.md to emphasize that a bundled jellyfish-2.2.0 is included

[tgac]

Update README.md to emphasize that a bundled jellyfish-2.2.0 is included

[maplesond]

This is fine, the KAT version of the modified jellyfish executable, libraries and manual is prefixed with "kat_" so there will be no conflicts with the existing version of jellyfish installed on your system.

[mmokrejs]

Still I would prefer to have this included in README.md. Also, I see seqan-2.0.0 is included.

[bjclavijo]

Martin, as both libraries have been included in such a way that they don't generate any conflict in the system, their license files are included where appropriate, etc. I think we're fine with this. We will try to enhance the read when we have all these details together.

[mmokrejs]

as both libraries have been included in such a way that they don't generate any conflict in the system

But the conflict happens once the binaries use the original jellyfish during execution. I propose the jellyfish is installed under a modified name, like jellyfish_kat. That means the binary, *.a, headers directory name, *.so, *.pc file at least.

[maplesond]

I'm not sure I understand. Everything has already been modified like you suggest... unless I'm missing something...

[mmokrejs]

Oh sorry, I answered from top of my head without checking the actual filenames. I should re-read the docs now or just check what the install procedure does.