Koeng101

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

3

PCR simulation should have circular as a attribute of the sequence getting input itself, not of the entire function.

Added slow5 parser

2

This PR will add a slow5 and blow5 format parser, from https://github.com/hasindu2008/slow5tools This won't implement the fast5 -> slow5 functionality, but will be able to read and write those files...

Methylation testing

1

People can get pissy when they don't check methylation when cutting with BsaI: https://ethanomics.wordpress.com/2013/06/28/bsai-worst-restriction-enzyme-ever/ "One of the sites had a 4 out of 5 bp match to the Dcm recognition...

Right now, the repeat fixer fixes one codon at a time, which is very inefficient. We should identify the largest repeats and then fix multiple places at once.

Codon table generation awkward

4

It is kind of awkward generating codon tables. For example, an external user would input something like this - ```go seq := poly.ReadGbk("data/pichia_chr2.gb") ct := seq.GetOptimizationTable(poly.GetCodonTable(11)) ``` It might be...

assistants API

6

**Is your feature request related to a problem? Please describe.** Today, OpenAI announced their assistants API. I would like support for this API in golang. https://platform.openai.com/docs/api-reference/assistants **Describe the solution you'd...

Each fragment in a PCR amplification should have a circular tag

1

https://github.com/TimothyStiles/poly/blob/f76bf05497cb89d5a48ab0a2ac41db9cfc425d12/primers/pcr/pcr.go#L170 Circular is used for all sequences. Should be on a per sequence basis.

slow5 doesn't detect newline

4

If there is a newline at the end of a slow5 file, the parser detects this as an additional line / read.

Failed to parse Saccharomyces cerevisiae S288C chromosome IX

8

the `

Pileup parsing deletion with .

4

I have the following read: ``` 57 510 C 5 ..,,. RD7HN 57 511 A 5 .-3TTG.-3TTG,-3ttg,-3ttg.-3TTG JC7H: 57 512 T 5 ***** @?8J: 57 513 T 5 ***** @?8J:...