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Hublabel#4870

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electricEpilith wants to merge 104 commits into
masterfrom
hublabel
Open

Hublabel#4870
electricEpilith wants to merge 104 commits into
masterfrom
hublabel

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@electricEpilith

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Changelog Entry

To be copied to the draft changelog by merger:

  • Add hub labeling to distance index, which allows efficient exact shortest distance queries even in "oversized" snarls
  • Bug fix for minimizer, significant speed improvement

Description

Adds hub labeling functionality to the snarl distance index.

electricEpilith and others added 30 commits November 12, 2025 14:32
@electricEpilith

electricEpilith commented May 8, 2026

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Dropped the hash tests. Moved refactor commits to hublabel-refactor.

@electricEpilith electricEpilith marked this pull request as draft May 8, 2026 21:37
@adamnovak adamnovak marked this pull request as ready for review May 15, 2026 19:26

@adamnovak adamnovak left a comment

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This looks pretty good. I found a couple places where it's not quite done and made suggestions.

I think the libbdsg changes also need to be finished, and then this needs to be made to point at the final libbdsg commit. Right now it's behind vgteam/libbdsg#239 by a few commits.

Comment thread src/subcommand/minimizer_main.cpp Outdated
Comment thread src/gbwtgraph_helper.cpp Outdated
Comment thread src/snarl_distance_index.cpp Outdated
electricEpilith and others added 11 commits May 23, 2026 15:11
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>

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This looks pretty good now. The only thing I think we really need to change is making sure we point at the actual libbdsg commit we want.

Comment thread src/subcommand/bench_dist_query_main.cpp Outdated
Comment thread deps/libbdsg
electricEpilith and others added 10 commits June 3, 2026 23:36
Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The docs-job ran git submodule update in place on submodules the CI
workspace left with stale origin URLs (a local mirror that is not a valid
repo on the runner). deinit alone did not fix it because it leaves the
cached gitdir under .git/modules/<path>, which update --init then reuses
with its stale file:// origin. Remove both the working tree and the cached
gitdir so each dep is re-cloned fresh from its canonical https URL, and set
protocol.file.allow=never to deny local transport entirely (CVE-2022-39253)
instead of the previous =always. Recurse only into libvgio, the one dep
whose Doxygen INPUT needs a nested submodule tree.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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2 participants