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Mutations still introduced when mutation rate is 0 #94

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harrytchild opened this issue Feb 15, 2024 · 3 comments · Fixed by #111
Closed

Mutations still introduced when mutation rate is 0 #94

harrytchild opened this issue Feb 15, 2024 · 3 comments · Fixed by #111
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@harrytchild
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I am looking to use NEAT to generate simulated reads with no mutations introduced, only sequencing error incorporated. In the config yml file, I have set the parameter "mutation_rate: 0". However, when I run NEAT with this config file, the program still introduces mutations to the reference before sampling reads. Here is an excerpt from the output:

2024-02-15 16:13:59,264:INFO:neat.read_simulator.runner:Beginning simulation.
2024-02-15 16:14:00,823:INFO:neat.read_simulator.runner:Generating variants for NC_006511.1
2024-02-15 16:14:07,082:INFO:neat.read_simulator.utils.generate_variants:Finished generating random mutations in 0.10 minutes
2024-02-15 16:14:07,082:INFO:neat.read_simulator.utils.generate_variants:Added 4658 mutations to NC_006511.1

Can you let me know how to set the config file so that no mutations are inserted before simulating reads?

@joshfactorial joshfactorial self-assigned this Feb 15, 2024
@joshfactorial
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I will look into this! That's definitely not the desired behavior!

@joshfactorial joshfactorial added the bug Something isn't working label Feb 15, 2024
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Okay, I did find a small bug related to this issue. Python was treating a 0.0 mutation rate as a "false" value in an unexpected place. I will push a fix of this to the main branch.

@joshfactorial
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The latest main branch changes have fixed this error. I was able to successfullly generate a 0 mutation fastq using mutation_rate: 0.0 and min_mutations: 0 in the config. Please let us know if you have any further problems with this.

@joshfactorial joshfactorial linked a pull request May 26, 2024 that will close this issue
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