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the bubbles #382

Draft

ekg wants to merge 3 commits into master from the-bubbles

Contributor

ekg commented Mar 28, 2022

Path-based bubble finding.

Goals:

fast bubble finding in complex graphs (linear/banded in reference length)
reference-based bubble finding
non-canonical bubble finding to resolve "snarl insensitivity" issue where the first variable site within a bubble is ignored
untangling approach used in vg deconstruct to ground coordinates and filter out ambiguous or conflicting observations, and possible integration of odgi untangle grounding
VCF output from odgi bubble
bubble chain finding

ekg added 3 commits

March 27, 2022 16:56


          stub implementation of bubble finder

de8959f


          simple path-based bubble finding

68b2c13


          update executable help text

63c00a8

AndreaGuarracino marked this pull request as draft

October 17, 2022 15:49

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