Updating version and changelog, adding GC Bias modeling#284
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Feature/add gc bias optimize
joshfactorial
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I also eliminated the temporary fasta file writing. |
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This looks to be the core of calculating GC bias and it looks like it makes sense to be for the most part, though I have to think a bit further about why rescaling is needed. Overall, the window-based approach makes sense to me.
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The getter functions we need to compute GC bias make sense to me!
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I will look more closely into the CDF sampling, but the rest of the script looks great and makes sense!
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It's basically what they were doing in NEAT 2
keshav-gandhi
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May 15, 2026
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Includes an update to the coverage function to use a CDF based approach instead of the generate and discard approach we originally had, this allowed us to incorporate GC Bias effectively, without falling into occasional infinite loops. Also includes several test updates and a new subfunction to generate a GC-bias model from real data (as in the original NEAT 2.1).