During pVACseq reruns, comparison of log files will throw an error if a newer version added a new argument

Open Beginner friendly
#166 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Assessment

Difficulty
2/5
Estimated time
1-3 hours
Newbie friendliness
70/100
Issue type
Bug
Clarity
Clearly specified
Activity status
Stale
Tech stack
python
Domain
backend

Research direction

Start in src/pvactools/lib/pipeline.py at print_log, especially the comparison around line 100. Check how current_inputs and past_inputs are built, then verify that a pVACseq rerun with a newer argument completes without a KeyError when the older log lacks that argument.

Written by the indexing model from the issue text.

Description

This will result in an error like this:

  File "/src/pvactools/lib/pipeline.py", line 100, in print_log
    elif current_inputs[key] != past_inputs[key]:
KeyError: 'phased_proximal_variants_vcf'

The solution is to first check whether key exists in both input lists.

Dominant language
Python
Stars
188
Forks
81
Avg merge
9d 17h
Merged PRs (30d)
6

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

More from griffithlab/pVACtools

All issues in griffithlab/pVACtools

Similar issues

More Python issues

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.