WIP Minigraph postprocessor - #2006

Merged

glennhickey merged 11 commits into

minigraph-cleanup

Sep 16, 2026

Commits on Sep 11, 2026

Optionally collapse inverted alleles after minigraph construction

glennhickey
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claude
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f3f3ddf
Pin cactus-gfa-tools to the branch carrying rgfa-collapse

glennhickey
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claude
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c600827
Bump cactus-gfa-tools to the fixed rgfa-collapse wiring

glennhickey
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claude
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464acad

Commits on Sep 12, 2026

Bump cactus-gfa-tools for the rgfa-collapse reporting fixes

glennhickey
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claude
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d0eef59

Commits on Sep 14, 2026

Give the collapse job fewer, wider minimap2 invocations

glennhickey
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claude
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4bcf2a4

Commits on Sep 15, 2026

Settle the collapse options, leaving the feature off by default

glennhickey
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claude
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381d9e8
Merge origin/master into minigraph-cleanup

glennhickey
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claude
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aaa0121
Make collapseInversions actually take effect in cactus-pangenome

glennhickey
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claude
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cbda279
Cover the --mgSplit paths with the collapse on, and pin the fix they found

glennhickey
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claude
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6d629ff

Commits on Sep 16, 2026

Merge origin/master into minigraph-cleanup

glennhickey
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claude
committed
d91ac75
Reconcile the collapse with master's --inGFA work, and reject the one combination that cannot work

glennhickey
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claude
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2fc4998