Joseph Lee

call-methylation returns non-CG methylated site?

4

I ran the example in https://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html. However, I noticed that some reported coordinates were not pointed to C/G base and probably shift -1 base. For example, in `methylation_frequency.tsv` ``` chr20...

分段推文建議

1

這個功能太好用了！ 希望能再加一些features 1. 將換行符號也一起推，這樣要寫bullet points或多行的圖形時會很方便！ 2. 即時換算目前的文字量是幾段的推文，可以避免貼url時斷掉 Thanks in advance!

Move files between s3 and local (copy and paste)?

3

**Describe the bug** Copy s3 file and paste in local folder is not working, and vice versa. **To Reproduce** 1. Copy file in s3 bucket (cmd+C) 2. Move to local...

Minimal filename completions for the unimplemented subcommands

2

For tools like bedtools, there are too many subcommands and not everyone is implemented for completion. Also most of them are not frequently used and maybe change by time. Can...

I'm trying to align some palindrome sequences, and there is a weird behavior of cigar string. ```python import parasail def test(): a = 'AAAAGACTTGGCTCGACAACGC' b = 'GCGTTGTCGAGCCAAGTCTTTT' # reverse complement...

bug: Extmark overlay on dimmed characters becomes blurry

1

### Did you check docs and existing issues? - [X] I have read all the vscode-neovim docs - [X] I have searched the existing issues of vscode-neovim - [X] I...

Add docker file for easier building dependencies and environment.

I am trying to add Roman numerals, but it failed when the length of value is 1. ```lua allow_caps_additions = { { "i", "ii", "iii", "iv", "v", "vi", "vii", "ix",...

bug/Wrong parsing of html, xml code blocks in markdown

2

**Describe the bug** HTML and XML code blocks in markdown are not parsed properly. Results: ~~~ HTML Example ```html Hello, World! This is a simple HTML example. ``` XML Example...

ORF prediction with non-standard genetic code sometimes are wrong.

3

I'm using the latest mfannot via docker image. I'm annotating a fungal mt genome with [genetic code 4](https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG4), and some of the ORFs were problematic. I have cross-validated with ncbi...