Comet v2024.01.0 yields empty results when using 'peptide_mass_tolerance'

[cbielow]

The reason is basically rooted in #59.
When using peptide_mass_tolerance = 10 in the param.txt then Comet will use

10 to -10 as mass tolerance boundaries (which yields an empty result), instead of -10 to 10.

Quickfix: specify

peptide_mass_tolerance = -10

which will negate the bug (not the go-to solution though).

The fix is easy, and probably part of #59.

Regression tests are highly valuable here, since they would have caught this early on.

[jke000]

Thanks for reporting all of these issues. I just committed a fix to restore backwards support for the retired peptide_mass_tolerance parameter. It got broken with commit c238fec which addressed proper application of the _upper and _lower parameter settings. Backwards support of this retired parameter was not part of my set of tests that I run before release but I just added this to my test suite. And regression testing will hopefully make it into the code someday. I'm going to close this issue with this comment and commit but reply if I missed anything.

[cbielow]

thanks for fixing this so quickly.
This will go into the next Comet release, I assume?
In the meantime I will implement the negation hack into OpenMS if it detects Comet v2024.01.0, so users will not notice.

[jke000]

Yes, this fix will be in the next release.