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Daniel-Liu-c0deb0t avatar Daniel-Liu-c0deb0t commented on August 16, 2024

Good point, this is an oversight on my part. I think it does matter in practice because chains of insertions and deletions makes finding the optimal alignment slightly more difficult for block aligner.

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RagnarGrootKoerkamp avatar RagnarGrootKoerkamp commented on August 16, 2024

One potential benefit here is that the actual edit distance of the generated sequence is probably a bit higher than in the completely uniform model. At least my intuition is that in your code the probability of mutations 'cancelling' each other is smaller.

Anyway, I'll likely write a linear time rust implementation for this soon.

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RagnarGrootKoerkamp avatar RagnarGrootKoerkamp commented on August 16, 2024

I've just pushed an implementation using ropes here, in case you'd like to reuse it. I'll likely package it separately at some point.

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Daniel-Liu-c0deb0t avatar Daniel-Liu-c0deb0t commented on August 16, 2024

Fixed the implementation of the rand_mutate function by using a slightly different approach than before.

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