whatshap phase: Make --indels the default

[marcelm]

I suggest to enable indel phasing by default. The option doesn’t have the best name anyway (it also works with "complex" variants/MNPs). By instead adding an --only-snvs option, that naming issue would also be solved.

This may require bumping the version to 2.0.

[marcelm]

Ping @tobiasmarschall @schrins Do you have an opinion on this? The option seems to work well enough and I think WhatsHap should aim to give the best possible phasing "out of the box", i.e., without providing any extra command-line arguments.

Raising this again because of #468, where @Npaffen was apparently not aware that --indels exists.

[schrins]

I don't see any problems so far by including indels by default. Not knowing about this option indeed came up multiple times now.