4.1 writing _uncalibrated.mzML for RAW files

[chambm]

I'm doing a data_type=2 GPF search. Is it supposed to always write the uncalibrated mzML even though I have:
write_calibrated_mzml = 0
write_uncalibrated_mgf = 0

[fcyu]

It always write the *_uncalibrated.mzML if the input is in .raw and .d because some downstream tools can't read them.

Best,

Fengchao

[chambm]

Can you make that an option? Not only are those files big but BiblioSpec currently prefers _uncalibrated.mzML over .RAW, even though it's capable of reading RAW. In this case for performance and space-savings we'd would want to prefer RAW. It would be easiest to achieve that by just not making the mzML in the first place, but in the short term I can just delete it before running BlibBuild.

[fcyu]

TBH, I don't want to add this option. We had this option before if I remembered it correctly, but there were just too many options, and we always need _uncalibrated.mzML with raw as input.

Best,

Fengchao

[chambm]

No problem, I can just the delete the files. I feel like since it's in the same vein as the other two options it would fit right in and it doesn't matter if there's 120 options or 121 options. :)

[chambm]

Wait what happens if the RAW location is read-only? Does it error or just skip the writing?

[fcyu]

That's correct, it prints something like Could not write XXX_uncalibrated.mzML. It will not affect MSFragger's result..

And I agree that it will be an issue because MSFragger also writes *.pepXML and *.pin files to that directory. I always want to change MSFragger to write the files to the result folder, but don't have time to do that.

Best,

Fengchao

[fcyu]

Hi Matt,

After a second thought, I decided to add the write_uncalibrated_mzml and removed the write_uncalibrated_mgf that is used nowhere. Let me know if you want to test the new version. Maybe can wait until #324 is also done.

Best,

Fengchao