Add --timeout-second and retry to callVariant

[zhuchcn]

Description

I have a transcript with 375 SNV/Indels and can not finish in hours. The limiting step is calling mislceaved peptides from the PCG, after cleavage. Setting a global max_variants_per_node doesn't make a lot sense to me, so I implemented a timeout function. So for each transcript, if it can't be finished in certain time, it will stop and retry with a lower max_variants_per_node (and additional_variants_per_misc).

The --timeout-seconds is added to callVariant and defaults to 30 minutes.

The --max-variants-per-node and --additional-variants-per-misc can accept multiple values now, and they will be used as the "retry strategy". And if we run out of the --max-variants-per-node values, it will continue retry with the previous value minus 1 until 0 and raise an error. For example, with --max-variants-per-node 7 5, the retries will be 7 -> 5 -> 4 -> 3 -> 2 -> 1 -> error (which should never happen).

--additional-variants-per-misc is slightly different. If we run out of values, 0 will be used. So by default it will be 2 -> 0

Closes #...

Checklist

• [X] This PR does NOT contain PHI or germline genetic data. A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem.
• [X] This PR does NOT contain molecular files, compressed files, output files such as images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other non-plain-text files. To automatically exclude such files using a .gitignore file, see here for example.
• [X] I have read the code review guidelines and the code review best practice on GitHub check-list.
• [X] The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
• [X] I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.
• [X] All test cases passed locally.

[lydiayliu]

Interesting, can you input something like --max-variants-per-node 7,7,7,5,5,5,3,3,3,2,2,2,1,1,1 and --additional-variants-per-misc 2,1,0,2,1,0,2,1,0,2,1,0,2,1,0 to get a grid search effect?

[zhuchcn]

You can, but this retry mechanism is only awakened when a transcript is timed out. Setting too many retry cycles will probably make the total run time very long. For example, if it ends up being finishable with 5-0, you will have to run 5 times before it. If we set --timeout-seconds to 900, it will take 90 minutes to finish this one (which isn't super bad).

Btw, I made these two arguments to accept multiple values, so you don't need to comma. Like this:

--max-variants-per-node 7 7 7 5 5 5 --additional-variants-per-misc 2 1 0 2 1 0