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…o's bundled version
…teration queries where appropriate
Stop deciding to exclude alt paths now. Only get sample names from haplotype-sense paths when we're not already using a GBWT.
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Changelog Entry
To be copied to the draft changelog by merger:
PathHandleGraphiteration functions. vg attempts to request the appropriate path senses when haplotype paths should be ignored for a particular operation.Description
In addition to some Makefile revisions (to stop clobbering our own
libhandlegraphwith the bundled one inlibvgio, and to treat thebuild_graphtest binary more like the other binaries), this has the code ingbwtgraphto stop hiding haplotype paths and haplotype steps, and documentation changes inlibhandlegraphto stop specifying that one should do that.It also has changes in
libhandlegraphto let you query multiple path senses at once more easily.Finally, this goes through all the places where we query for paths, and tries to fix the ones that oughtn't include haplotype paths to specifically not request them. This part was mostly done by Anthropic Claude, and despite a fair amount of badgering it never really gained a great understanding of what was going on, so I had to do a lot of manual figuring in at least one place and it's possible others are still wrong.
This does pass the command-line tests when I run it, so we must be mostly pulling the right paths in the right places.