Revert path sense filtering in clip, depth, simplify and traversal_fi…#4830
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glennhickey merged 1 commit intomasterfrom Feb 13, 2026
Merged
Revert path sense filtering in clip, depth, simplify and traversal_fi…#4830glennhickey merged 1 commit intomasterfrom
glennhickey merged 1 commit intomasterfrom
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…nder The "no secret paths" commit (2315642) mechanically replaced for_each_path_handle() with for_each_path_of_sense({REFERENCE, GENERIC}) across the codebase, which inadvertently excluded haplotype paths from depth calculations, path enumeration, and path destruction in several tools. This caused regressions where more content was clipped (clip), depth was underreported (depth), haplotype paths survived when they should have been removed (simplify), and haplotype path traversals were lost (traversal_finder). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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…nder
The "no secret paths" commit (2315642) mechanically replaced for_each_path_handle() with for_each_path_of_sense({REFERENCE, GENERIC}) across the codebase, which inadvertently excluded haplotype paths from depth calculations, path enumeration, and path destruction in several tools. This caused regressions where more content was clipped (clip), depth was underreported (depth), haplotype paths survived when they should have been removed (simplify), and haplotype path traversals were lost (traversal_finder).
I noticed this when updating to vg 1.72.0 in Cactus caused its tests to start failing.
Changelog Entry
To be copied to the draft changelog by merger:
vg clip,depth,simplifyand potentially some uses ofdeconstructandcall, that results from a change that ignores haplotypes in .vg files (to be consistent with how .gbz files would have been treated).