Closed simone-pignotti closed 5 years ago
Totally, I'll add the scoring methods / enzymes to the help messages. I'm traveling until Thursday but should have the fixes for the discover command line option bug in quick. Thanks for the error reporting, it's super helpful.
No problem, glad that helps!
I think both issues above should be fixed in version 1.9.1. I'm also happy to move the scoring descriptions around, for now I put them with the help for -scoringMetrics, but maybe they should go at the top.
Thanks, the discovery help works now. On the other hand, the -scoringMetrics one includes the output column names, which sometimes differ from the cmd line option (Hsu2013
instead of hsu2013
still works because the match is case insensitive, but Doench2016CFDScore
instead of doench2016cfd
doesn't).
Also, in discover
the default -flankingSequence
is 6, not 10, and the format of -positionOutput
is not documented in the wiki (easy to figure out though).
Other options that I have tried quickly but I am not sure whether they are working:
discover
=> -markExactGenomeHits
score
=> -countOnTargetInScore
score
=> -maxReciprocalMismatch
But this is going far from the original topic. I can close this once the -scoringMetrics
is fixed and open new ones with more details as soon as I have time.
Thanks for catching that; I've taken an overdue pass at cleaning out any old command-line args in version 1.9.2. The markExactGenomeHits option was redundant with the current scoring options, so I took that out. The other options listed above are still active. I'll also add some documentation about the output formats in general, which are certainly lacking. Thanks for the heads-up!
Great, thanks a lot to you!
Hi, while for every other command you can get the help message by calling it without arguments, the
discover
one exits with an error because it tries to open the DB header.header
(I guess the default value of the database parameter is the empty string). Should be a very quick fix. Concerning all the help messages, I think it would be useful to include the list of scoring methods and enzymes, even without description, so that one can easily recall the exact parameters without checking the wiki.Thanks for this awesome tool, it's one of a kind! Simone