Allow disabling 3' Shifting in the rest server

[janeliutw]

@holtgrewe,

I work on @CarlosBorroto 's team, and this PR is continuing the discussion on #551 . I saw that there's a fix(#553) to enable --no-3-prime-shifting argument for annotate-pos command, thanks for fixing it! In our use cases, we use the rest server to annotate variants., so we are hoping to have an option to disable 3' shifting on the rest server as well.

We noticed that when running rest-server command, --no-3-prime-shifting is already an optional argument.

MDMBJALIU:target jliu$ java -jar jannovar-cli-0.40-SNAPSHOT.jar rest-server --help
usage: jannovar-cli rest-server [-h] [--host HOST] [--port PORT] -d DATABASE [--show-all] [--no-3-prime-shifting] [--3-letter-amino-acids] [--version] [--report-no-progress] [-v] [-vv] [--http-proxy HTTP_PROXY]
                    [--https-proxy HTTPS_PROXY] [--ftp-proxy FTP_PROXY]

it's just not actually being hooked up yet. So in this PR, we proposed a change to enable --no-3-prime-shifting in the rest server:

• Enable --no-3-prime-shifting argument in the Rest Server.
  To disable shifting variants towards the 3' end of the transcript, run the rest server with --no-3-prime-shifting argument.
  For example,
  java -jar jannovar-cli-0.40-SNAPSHOT.jar rest-server -d data/hg19_refseq.ser --no-3-prime-shifting

Additionally, we proposed a new query param that allow a user to disable 3 prime shifting in an api request.

• Accept no-3-prime-shifting as an api query param to temporarily disable 3 prime shifting.
  For example,
  https://{base_url}/annotate-var/refseq/hg19/chrX/108924495/C/CTTA?no-3-prime-shifting
  Notice that this query param is only for disabling 3' shifting, so if will only take effect if the rest server is running with 3' shift enabled.

Please let me know your thoughts on the changes or if I miss anything. Thank you!

[visze]

LGTM. thank you! @holtgrewe any comments?

[CarlosBorroto]

Hi @holtgrewe @visze, we are wondering what timeline would be reasonable to expect for this PR to get merged and included in a release? We understand there are no hard promises we should expect, just trying to decide if we should go with an internally built jar for a bit, while this gets fully baked into upstream.

[holtgrewe]

Again - thanks a bunch! I will merge this together with your other PR and then make a release.