Bigwig

[ejacox]

Adds server code to implement the continuous sequence annotation service as part of ga4gh/ga4gh-schemas#769.

[david4096]

Really stellar code! Just took a look and it follows the existing patterns clearly.

Noting that the only failing test is test_constraints, which is by design.

[david4096]

Does it get used?

[ejacox]

Not anymore. Removed.

[david4096]

This is a very clever usage of the existing tools to support the BigWig format using the reader you wrote! You note the issues of running a subprocess. It seems like you opted to use the existing python tools, which I think is a very sane choice. Would you like to leave this in for future feature support? Is it used?

[david4096]

Would you please add an entry to the templates/index.html for the continuous sets? Something like https://github.com/ga4gh/server/blob/master/ga4gh/server/frontend.py#L184

Although it is a problem in the reminder of the API, we might choose to not adopt the assumption that a reference set must be set on the continuous set. We'll do that in a later PR (#1528)

[david4096]

I had to install the libcurl4-gnutls-dev to successfully install PyBigWig. I wasn't able to replicate this issue uninstalling the package though. PyBigWig seems to want to have curl-config around for accessing remote BigWig files.

[david4096]

Congratulations @ejacox this is a sizable addition to the protocol and does a good job at making some of Jim Kent's (and other's) work available to a wider community!