Open nh13 opened 4 years ago
Dear Nils (@nh13 ),
Thank you for your quick test of PuffAligner.
The particular items you pointed at in this issue are definitely something that requires our immediate action to resolve so that the help manual of the tool is easy to interpret by the user. The biggest issue is the automatically generated help produced by the argument parsing library we are using, clipp, exhibits the issues you raise regarding duplicate options in the way it generates the default help messages. We're looking into if there is a way to fix this within clipp, and may otherwise consider changing the argument parser we use.
That being said, we hope to have this resolved one way or the other in a few days. We are currently in the process of merging the cigar-strings
branch where Puffaligner lives and the develop
(which we use as an external library for the selective-alignment in salmon). We anticipate it will take a few days to test and guarantee that the performance and the accuracy are not changed by either some specific optimizations in cigar-string
branch or merge conflicts. After that, we will continue resolving these issues on the (merged) develop branch. We will ping back here when the develop branch is updated with the improved help messages and options.
Thank you again!
And I would suggest please if when e.g. pufferfish index --help
, only show the index
help and relevant options, same as other command line programs already do with sub command help. This will probably already eliminate the number of duplicate options seen in the help.
Four suggestions based off of 8c24fb15335825bc54d3548db23009c1ca479711:
The "-h" or "--help" options get a strange error. If they aren't implemented, then shouldn't the tool complain "no such option exist" versus the following?
The help message has duplicate entries, for example:
The help message has two options for the same flag:
Can you add the default/current value to each option? For example, I assume that
allowSoftclip
is off by default (end-to-end alignment), but if the option could output:Full output of the help message: