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Improve the degree to which SnarlDistanceIndex actually implements SnarlDecomposition #247

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Merged
adamnovak merged 18 commits into from
Oct 16, 2026
Merged

Improve the degree to which SnarlDistanceIndex actually implements SnarlDecomposition #247

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5e2846b
List a chain's children in the order its traversal visits them
Oct 15, 2026
b4e0424
Give a looping chain's end bound a start-to-end or end-to-start trave…
Oct 15, 2026
cb08892
Make stepping left the inverse of stepping right in follow_net_edges
Oct 15, 2026
8b22e17
Let a chain turn around only where a walk from its bound can
Oct 15, 2026
a5907e9
Work out snarl and chain tips innermost first
Oct 15, 2026
916a43c
Make a trivial chain's traversal from the traversals of its node
Oct 15, 2026
d5046c9
Make get_parent() of a sentinel give its snarl START_END
Oct 15, 2026
7ddae47
Give every realizable traversal a walk can enter in follow_net_edges()
Oct 15, 2026
90c3c3c
Explain the snarl decomposition fixes in the decomposition's own terms
Oct 15, 2026
d625ba5
Say what the tip pass's vectors hold and what each walk step checks
Oct 15, 2026
47f03c2
Rewrite the snarl decomposition fix comments to read on one pass
Oct 15, 2026
ca6b30f
Rewrite the snarl decomposition fix comments for a human reader
Oct 15, 2026
8f97707
Explain why repack() and zero_from() may skip the element-wise copy
Oct 15, 2026
83a6f40
Zero entries exposed by PackedVector::resize() growing within capacity
Oct 15, 2026
f010c41
Take tip flags from the temporary index, and apply review suggestions
Oct 16, 2026
c672c32
Drop the TODO about oversized snarls lacking tip flags
Oct 16, 2026
ded22a7
Apply review comment suggestions and note the looping chain listing
Oct 16, 2026
ff6c2dd
Add note about least-weird decision
adamnovak Oct 16, 2026
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