Koeng101

PCR simulation should have circularity as an aspect of the sequence itself, not of the entire function

1

[link](https://github.com/bebop/poly/issues/225) This should obviously be implemented.

Change WriterTo to make a builder first

1

Here is an example written by ChatGPT: ```go func writeHD(w io.Writer, hd map[string]string) error { // Define the order of specific keys orderedKeys := []string{"VN", "SO", "GO", "SS"} // String...

Default codon tables

1

[link](https://github.com/bebop/poly/issues/247) This is still a feature that is needed, and needed even more for the basic API!

https://github.com/bebop/poly/pull/411 This is a cool feature. Let's merge.

minimap2 + samtools wasm

1

I want minimap2 + samtools integrated into dnadesign so that alignment can take place without going to C / bash. https://biowasm.com/cdn/v3/minimap2/2.22 It can definitely be done, just will take some...

slow5 version should be in the Header, not the HeaderValue. In addition, HeaderValues don't take care of ordering / multiple read groups right now ```go type Header struct { HeaderValues...

Stop codons are usually "*" not "x"

3

https://github.com/CamelCaseCam/CadBerry/blob/36dad3c8c382a2da26ca78d61ff2a99aaf7310f2/CadBerry/GILBuildEngine/src/GIL/Compiler/CodonEncoding.cpp#L74-L76 Small nitpick : stop codons are usually represented with "*", not "x"

I'd like the python version of dnadesign to be runnable in the browser, so people can immediately test out how it works! https://github.com/nalgeon/codapi/blob/main/docs/add-sandbox.md Seems really promising. Basically, the idea is...

I don't like that go-cmp is in the source tree. Seems kinda complicated. Noting here that I want to purge it from the source tree. Then, dnadesign will not have...

Add tokenizer

2

This PR is creating a tokenizer in the dnadesign lib. This is primarily for tokenizing amino acids for consumption of an LLM - in particular, llm.c.