Add a "noisy" profile

[marcelm]

As suggested in the multi-context seeds (MCS) paper, we should add a profile that sets these parameters: -k 16 -s 12 -l 2 -u 2

One would choose this instead of setting a read length (with -r). On the command-line, we could handle this in two ways:

• Add a new option and do not allow it to be used together with -r. BWA-MEM and minimap2 use -x to change the profile, but -x is already used in strobealign. Option -P would be available. Available lower-case character options are: adegjnqwyz
• Or, extend the -r command-line option so that one can write the name of a profile instead of a read length, as in -r noisy

I’m leaning towards the second option at the moment. It’s slightly more difficult to implement, but may be easier to use.

[ksahlin]

No strong opinion on which is preferred. We may add other modes (e.g., aDNA, SV) if the method don't diverge too much from the current mapping workflow, so that is one thing to plan ahead for.