fix(preprocessing): GenerateSequenceTableViaFile - enforce exact match on TSV/FASTA file pairs

[anna-parker]

resolves #607

Summary

Preprocessing pairs sequences and metadata (or references) when they have the same file name minus extension (e.g. dir/gene12.fasta and dir/gene12.tsv). Given a metadata/reference file the generateSequenceTableViaFile function is used to find the corresponding fasta file.

However, the function did not match on the exact base stem of the files, it just checked if the start of the stems matched, meaning that gene12.tsv could be matched with gene1.fasta. This patch enforces an exact match on the file base stem. As files can have multiple extensions e.g. gene1.fasta.gz I create the getBaseStem function to compute the base stem of a file recursively, this removes all extensions from a file path and leads to correct pairing of files.

PR Checklist

• All necessary documentation has been adapted or there is an issue to do so.
• The implemented feature is covered by an appropriate test.

[github-actions]

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Changelog:

0.2.23 (2024-10-10)

Bug Fixes

• preprocessing: enforce exact match on file base stem when pairing sequence and metadata when processing from file (0e09bb6), closes #607

[fengelniederhammer]

LGTM

Could you please squash your commits, add a meaningful commit message that looks good in the changelog (explaining to unknowing users what happened) and make sure that the issue also appears in the changelog(via resolves #... in the message footer)?