When pinning ancestor, treat it as an outgroup#1945
Open
glennhickey wants to merge 2 commits into
Open
Conversation
… option) When the root's sequence is supplied -- cactus-blast/cactus-align --includeRoot, or the integrated cactus when an ancestor sequence is given in the seqfile -- cactus's pairwise chaining previously treated that pinned root as an extra ingroup. Ingroups that align better to each other than to the (often deeper) root then grab each other as their primary alignments and starve the root, collapsing its coverage to its descendants -- the bridge connecting a re-aligned subclade to the rest of the alignment after halReplaceGenome. Treat the pinned root as an outgroup instead, via a new <blast includeRootAsOutgroup> config option that defaults to on. This changes the default --includeRoot behaviour everywhere make_paf_alignments sees a supplied root (cactus-blast and the integrated cactus progressive path alike); it is blast/PAF-side only, so the consolidated/HAL output is unchanged in structure. To restore the old ingroup behaviour, pass a custom --configFile with includeRootAsOutgroup="0". Verified on the evolver (human,mouse,rat)Anc1 multifurcation: with the default config, --includeRoot alone gives root->mouse coverage 464k (73%); with includeRootAsOutgroup="0" it falls to 125k (20%), and mafComparator vs the ground-truth alignment improved both precision and recall. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…ubtree For a given --root ancestor (default: the HAL's tree root), export the ancestor and every genome below it as bgzipped per-genome FASTAs (one parallel Toil hal2fasta|bgzip job each) and write a matching seqfile. The ancestor's own sequence is included, so the output is ready to re-align and pin a subclade with cactus-blast/cactus-align --includeRoot. The HAL is symlinked into the jobstore and read by each per-genome job via symlink, and each job's disk is sized to its genome rather than the whole HAL, so this scales to large HALs without copying them once per genome. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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
1 participant
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 keeps the pinned ancestor (via
--includeRoot) out of the chaining a bit which should help increase coverage in some cases.Also adds
cactus-hal2seqfilewhich is a convenience tool for helping update existing alignments (will develop this a little more in future PRs)