Reduce excessive path indexing

[adamnovak]

Changelog Entry

To be copied to the draft changelog by merger:

• vg find -Q/--paths-named is now deprecated due to its partial-Protobuf output
• vg find will now index its target paths but not other haplotype paths.
• vg should no longer position-index haplotype paths unnecessarily in commands using the PathPositionOverlayHelper.

Description

This should fix cases where using the PathPositionOverlayHelper was making us index all haplotype paths.

I'm not sure if more commands need to be patched like vg paths to send along the names of haplotype paths they're actually interested in, to let queries on haplotype paths work. But we've only been indexing all the paths for a few months, and before that I think the behavior before that was for those queries to mysteriously give wrong answers.

[adamnovak]

I think we might need to fix vg stats --snarl-sample; I'm not sure it's under test with non-reference samples.

[adamnovak]

This uses vgteam/libbdsg#241 in libbdsg.

[adamnovak]

OK I went through all the subcommands using PathPositionOverlayHelper and I think I've fixed them all to ask to index the right paths.

The one I couldn't do yet was vg inject; now it can only inject into reference paths, since we don't have a great way to load the BAM header without the graph being ready.

We already have a lockout for that:

vg/src/alignment.cpp

Lines 590 to 600 in 1d90c0b

	// TODO: Decide we need to positional-index this path? Make
	// PackedReferencePathOverlay take a collection of paths to
	// index and use this one?
	#pragma omp critical (cerr)
	std::cerr << "error[vg::parse_tid_path_handle_map] Path " << target_name
	<< " referenced in header exists in graph, but as a haplotype."
	<< " It is probably not indexed for positional lookup. Make the"
	<< " path a reference path"
	<< " <https://github.com/vgteam/vg/wiki/Changing-References>"
	<< " and try again." << std::endl;
	exit(1);

This should be ready to merge when CI passes.