CAGE support

[siebrenf]

Adding to a PR from a fork is weird. @BrancoHeuts, do you have some test data I could run with this?

Added:

• CAGE file doesn't have to be a tsv anymore, as long as its a 2-column table.
• support for using regions and pfmscorefile (that was way harder than I thought)
• more checks (duplicate regions in the CAGE data, mismatches between CAGE data/regions/pfmscorefile)
• custom window sizes (same as for the other data types)
• automatic downloading of the remap bigwigs from zenodo.

Fix:

• CAGE Remap coverage is now calculated over the normalized regions
• tests

Still missing:

• the CAGE models folder in the database

[siebrenf]

@BrancoHeuts, did I add the correct motif files (CAGE_motif and CAGE_average_motif)?

[codeclimate[bot]]

Code Climate has analyzed commit 2a3a78b1 and detected 1 issue on this pull request.

Here's the issue category breakdown:

Category	Count
Complexity	1

The test coverage on the diff in this pull request is 69.7% (50% is the threshold).

This pull request will bring the total coverage in the repository to 60.6% (0.3% change).

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