Don't use special characters in tmp file names

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Assessment

Difficulty
2/5
Estimated time
1-3 hours
Newbie friendliness
72/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Active
Tech stack
python
Domain
backend

Research direction

Start by locating the temporary-file path construction used after prediction algorithms, then read the normalization method in pvactools/lib/output_parser.py around line 249. Apply the same normalization before constructing the path and verify that alleles containing *, : or / no longer produce special characters in temporary filenames.

Written by the indexing model from the issue text.

Description

Specifically the tmp files that get written after calling prediction algorithms contains the allele in their name. These can have *, :, and / as special characters. We should use a method like https://github.com/griffithlab/pVACtools/blob/master/pvactools/lib/output_parser.py#L249 to normalize the allele before constructing the tmp file path.

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

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