Merged
Conversation
Adds augref.cpp/hpp implementing AugRefCover, which computes augmented reference paths (altpaths) that cover haplotype-only regions of the graph. Integrates into vg paths with --compute-augref, --min-augref-len, --augref-sample, and --augref-segs options. Includes test GFA fixtures for dangling nodes and star allele clusters. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Refactors TraversalSupportFinder and TraversalClusters to support nested snarl traversal. Adds augref path filtering to prevent augref paths from anchoring snarl decomposition. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Simplifies deconstructor by removing legacy nested snarl logic and adding star allele (-R) option for top-down nested decomposition. Adds RC/RS/RD info tags, improves memory usage for large graphs, and updates tests for nested and cyclic variant structures. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Implements NestedFlowCaller which processes snarls top-down, recursing into child snarls to resolve nested variants. Adds -R option to vg call for star allele / nested calling mode. Includes triple-nested test fixture and comprehensive call tests. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Remove get_step(), get_parent_intervals(), print_stats() from AugRefCover and extract_child_traversal() from FlowCaller — all defined but never called. Remove unused ref_path_to_copy member variable and fix stale comment. Remove duplicate protected: specifier in augref.hpp. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
glennhickey
force-pushed
the
altpaths
branch
from
6dbaa5b to
72a8af2
Compare
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This is a revival of the now ancient #4113, but instead of using weird gymnastics to keep subpath intervals (a ala rgfa), it simply adds the new contigs to the existing linear reference they're derived from, leaves them REFERENCE sense, and adds a little suffix.
The cover is still computed in
vg paths.vg callandvg deconstructare now changed to work with these (optinonally).There's still some work before merging, most importantly: