Continuous dev-branch, setup travis-CI and codecov

[DennisSchmitz]

Instead of having a brach per version, @florianzwagemaker suggested to use a continuous dev-branch. Likewise, we should setup Travis-CI to make sure that every commit and merge functions properly (see here and here).

The Travis-CI should also be connected to codecov. Lastly, Travis-CI and codecov should be added as badges to the README as a means of relaying testing status.

[DennisSchmitz]

I've linked Travis-CI to this repo. But debugging a first Travis-CI test requires Docker and Docker isn't allowed on our grid. I've asked for a workaround, will update it afterwards.

Likewise, I've linked codecov to my GitHub. However, it's only free for public repo's. Once this repo is public, and Travis-CI is setup, I'll link it to this repo.

To be continued.

[DennisSchmitz]

Tests:

• Build test
• Input filename test:
  [sample]_R[1|2].f[ast]q
[sample]_[1|2].f[ast]q
[sample]_R[1|2]_001.f[ast]q
[sample]_[1|2]_001.f[ast]q
[sample]_R15_[ATCG]_R[1|2].f[ast]q
[sample]_R15_[ATCG]_[1|2].f[ast]q
[sample]_R15_[ATCG]_R[1|2].f[ast]q
[sample]_R15_[ATCG]_[1|2]_001.f[ast]q
[sample]_R15_[ATCG]_R[1|2]_001.f[ast]q

Input dataset:

• Public Cameroon dataset or maybe simulate a smaller set.
  • Check if all the log files are empty/non-empty (depends on the submodule) and compare this to a successful run.