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Revert PR #472 "Always pick first syncmer as base" #479

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merged 8 commits into from
Jan 29, 2025
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@marcelm marcelm commented Jan 28, 2025

... because of a decrease of accuracy in our tests for CHM13 (mostly at telo- and centromers).

As discussed by e-mail, the problem is likely because non-canonical randstrobes, as introduced by #472, lead to biased filtering of overrepresented randstrobes: Before #472, that is, with canonical randstrobes, we would treat a randstrobe and its "reverse complement" (its version with both strobes swapped) the same. A randstrobe in the query would thus be considered overrpresented if the corresponding sequence or its reverse complement were overrepresented. With #472, this was no longer the case and whether a randstrobe is filtered or not now depends on whether it is overrpresented in the orientation that it has in the query.

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ksahlin commented Jan 28, 2025

Approved!

@marcelm marcelm merged commit c0695b0 into main Jan 29, 2025
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@marcelm marcelm deleted the revert-basehash branch January 29, 2025 22:11
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marcelm commented Jan 29, 2025

The reverted changes are now in branch base-first and could be re-applied if we solve the accuracy problem.

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