[FIX] simplify passing file extensions to the validator

[joergi-w]

Currently, we manually collect valid file extensions from the different file formats. I found a simpler way to achieve this.

I found that we cannot read compressed sequence files because they are rejected by the validator, and SeqAn has already an issue for that: seqan/sharg-parser#77
Maybe we can push this issue a bit more into attention, as also other apps (like Mars) suffer from that.

[codecov]

Codecov Report

Merging #170 (7d1c124) into master (d14e155) will increase coverage by 0.21%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     seqan/seqan3#170      +/-   ##
==========================================
+ Coverage   96.48%   96.70%   +0.21%     
==========================================
  Files          19       19              
  Lines         797      789       -8     
==========================================
- Hits          769      763       -6     
+ Misses         28       26       -2     

Impacted Files	Coverage Δ
src/iGenVar.cpp	100.00% <100.00%> (+1.65%)	⬆️
src/variant_detection/variant_detection.cpp	93.97% <0.00%> (ø)

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[joergi-w]

The relative code coverage is lower, because I deleted some lines that had been covered by tests. But I didn't introduce new uncovered lines, so I don't agree that the check fails.

[SGSSGene]

I wasn't aware that seqan3::input_file_validator<seqan3::sequence_file_input<>>{} exists. This is very cool! 😮

[SGSSGene]

The relative code coverage is lower, because I deleted some lines that had been covered by tests. But I didn't introduce new uncovered lines, so I don't agree that the check fails.

Yes, I agree with you!

[Irallia]

If you are very motivated, you could add tests for the two uncovered lines in the iGenVar.cpp. But we can also leave it as it is and merge.

[joergi-w]

Sure, I'm already thinking about these tests. The problem is that the file validator already checks the existence, writability, and file extensions of the given paths – so I cannot think of any scenario that passes the validator and fails afterwards in iGenVar.cpp.

[Irallia]

Yes you're right. Than we should maybe just take it out of the coverage with:

// LCOV_EXCL_START
some code...
// LCOV_EXCL_STOP

[joergi-w]

Okay, done!