Library format checking for stranded libraries gives uninformative debugging messages about salmon HOT 2 CLOSED

@mdshw5 --- Salmon has definitely become less "complain-y" in the newer versions. That is, it will no longer spew out error messages for all of the fragments that show up in an unexpected orientation. However, the summary statistics are currently very "summary". There is a file in the quantification directory called libFormatCounts.txt that summarizes the number of alignments seen in the different orientations etc.

However, I really like your idea of recording the "violating" transcripts. That is, we could maintain some "threshold" beyond which if there are these many "incorrectly" mapping fragments for a transcript, the transcript is recorded and reported to the user as potentially being in the wrong orientation in the index.

from salmon.

I still like the idea of tagging potentially violating transcripts, but I think that the existing issue is reasonably well-resolved with the combination of (1) the new format of reporting incompatible mappings (i.e. if there is any compatible mapping of a read, then the entire read is considered as "compatible") and (2) the ability to write the actual mappings out, so that they can be inspected if desired.

from salmon.