trishorts
trishorts
i'll look at it.
can you get me one or two of the mzmls that i can use for trouble shooting?
not sure if this is the big problem but the sample file you gave me has an empty scan that is throwing an error:  it is scan 7192 
The second problem I see is that one column header is fileidx instead of file_idx. Maybe the the column header changed in the output? I can make a pull request...
The third problem i see is in the protein id column. We need to be able to assign a protein to each psm. The conventional format that you showed me...
The one open question I have is still if we can read the paths that you have. I generally don't put the full path in the file_idx column. But then...
Manually deleting empty scans is problematic b/c of missing scan numbers. We do see dead scans on fast instruments. We like to throw errors where there is a problem w/...
> Regarding the protein IDs, unfortunately we have no control over what naming scheme our users employ. All we do is take the IDs from the FASTA file. If there...
> Regarding the missing scan problem, I agree that it would be nice if the software could issue a warning in that case. If you don't like that, an alternative...