Remove vg sift (been deprecated since 2020)

[faithokamoto]

Changelog Entry

To be copied to the draft changelog by merger:

• vg sift is removed

Description

vg sift was deprecated in 2020 by #3136 and has since only really been "updated" by me, when I tweaked all the subcommand files for better option parsing etc. It is at its fundamental level just a GAM filterer. We already have vg filter for that, and indeed you could use vg filter --tsv-out plus some extra parsing to get e.g. reads with a bunch of softclips.

So this ends up being a bunch of code that we don't maintain nor use, for over five years. I propose deleting it. vg sift depended largely on a Filter object from src/filter.cpp/.hpp, and a lot of that got tossed too. The remainder is a small collection of functions that are less filtery and more standard Alignment handling; might make more sense to hand them over to the Alignment class?

[faithokamoto]

Oh also vg sift is at least somewhat broken, e.g. see #2199

[faithokamoto]

I realized the remaining parts of src/filter.* were only used in a genotype_svs() function which seems to have never been implemented, just stubbed in via comments. So I took that out too. If we want to have that functionality, we should put it in properly.