The only place I could find the term "sampled suffix position" (or even "sampled position" or "suffix position") used was in the help output for the -k option.
Also why the -threads option is only valid for when k > 1 is not clear. This in turn makes it even more difficult to understand why there is both a -threads and a -qthreads option.
I would have just ignored the existence of the option, except that the default examples given in the help both use a non-default option for k.
Here is the most basic question one could ask which isn't clear to me based on the documentation:
does a higher value of k lead to increased computational expense but better/more accurate results?
or does a higher value of k lead to decreased computational expense but worse/less accurate results?
The fact that multi-threading is only an option when k > 1 suggests the former. At the same time, since it apparently has something to do with "sparseness", it also seems plausible that k > 1 would lead to worse output.
Any improvements to the documentation would be greatly appreciated and would make me feel more confident recommending Mummer to colleagues.
Referring specifically to the
-koption of themummercommand.I searched on Google, as well as in the complete Mummer documentation at https://github.com/mummer4/mummer/blob/master/docs/maxmat3src.pdf
The only place I could find the term "sampled suffix position" (or even "sampled position" or "suffix position") used was in the help output for the
-koption.https://github.com/mummer4/mummer/blob/6c0da4101a55a0f89ecd00a5e569501a9a9f9ecd/src/essaMEM/mummer.cpp#L378
Apparently the
-koption is valid only for-maxmatch, but it is not clear why https://github.com/mummer4/mummer/blob/6c0da4101a55a0f89ecd00a5e569501a9a9f9ecd/src/essaMEM/mummer.cpp#L231Also apparently the
-koption has something to do with "sparseness", but again it is not clear why https://github.com/mummer4/mummer/blob/6c0da4101a55a0f89ecd00a5e569501a9a9f9ecd/src/essaMEM/mummer.cpp#L301Also why the
-threadsoption is only valid for whenk > 1is not clear. This in turn makes it even more difficult to understand why there is both a-threadsand a-qthreadsoption.I would have just ignored the existence of the option, except that the default examples given in the help both use a non-default option for
k.https://github.com/mummer4/mummer/blob/6c0da4101a55a0f89ecd00a5e569501a9a9f9ecd/src/essaMEM/mummer.cpp#L391 https://github.com/mummer4/mummer/blob/6c0da4101a55a0f89ecd00a5e569501a9a9f9ecd/src/essaMEM/mummer.cpp#L397
Here is the most basic question one could ask which isn't clear to me based on the documentation:
The fact that multi-threading is only an option when
k > 1suggests the former. At the same time, since it apparently has something to do with "sparseness", it also seems plausible thatk > 1would lead to worse output.Any improvements to the documentation would be greatly appreciated and would make me feel more confident recommending Mummer to colleagues.