Comments (4)
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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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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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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Fixed the implementation of the rand_mutate
function by using a slightly different approach than before.
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Related Issues (20)
- Support alignment of protein sequences containing "*" HOT 1
- Option to reuse memory when block aligner is reallocated
- Support Alignment of DNA sequences with C API HOT 1
- Neon and related HOT 4
- Is using -0.5 as extend penalty supported? HOT 2
- Is there a reason gap_open has to be > gap_extend and not >= gap_extend? HOT 3
- Custom AAMatrix from C API? HOT 7
- Thoughts on relation to / comparison with WFA HOT 1
- Use staticlib
- Investigate performance regressions
- question on block aligner score and lowest identity allowed to be accurate HOT 6
- Realignment
- fuzzy text finding HOT 7
- `cargo.toml` in `c` directory is detected as duplicate package HOT 1
- Question: Syntax for modifying the nucleotide scoring matrix HOT 3
- semi-global alignment HOT 6
- Try out convergence of traceback pointers
- Advice on setting for short query in long reference search HOT 5
- [BUG] Incorrect index calculation for score matrix setter HOT 7
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