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RFC: Should we migrate to fully-justified alignments?
When aligning sequences with indels in repeat regions, the alignment is ambiguous. Most aligners implicitly right or left shuffled gaps, but this choice is arbitrary: the real region of ambiguity spans from the left extreme to the right extreme. The result is that it’s hard to know whether a particular region is within an ambiguity region.
Proposal: Based on work from NCBI, GA4GH adopted fully-justified normalization for the GA4GH VR specification.
Migrating UTA alignments to fully-justified would allow relatively simple tests for whether a variant overlaped a region of ambiguity.
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This issue was closed by stalebot. It has been reopened to give more time for community review. See biocommons coding guidelines for stale issue and pull request policies. This resurrection is expected to be a one-time event.
This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 7 days.