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                                            Chang Ye

MD string for second reads

This bug still exists in the latest version of the `mappy` package. I believe it is a crucial issue, and users should be warned about it if it is difficult...

Replace pkg_resources with importlib_metadata

Same issues for python 3.12.

nvtop --No GPU to monitor.

I’m experiencing the same issue on Arch Linux, but nvitop works and might be a good alternative. https://github.com/XuehaiPan/nvitop

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Hi, I tried both 6.5 and the 7.0rc

base-depth become extremely slow when calculating highly covered site.

`perbase-base-depth 0.8.5`

base-depth become extremely slow when calculating highly covered site.

I did test samtools mpileup and my customized pipeup script using rust-htslib. The speed is not fast but acceptable. It took 0.5s for samtools mpileup. ``` samtools mpileup -f debug.bam...

base-depth become extremely slow when calculating highly covered site.

I waited more than 30 mins, but perbase is still running. I use all the threads, and there is no IO or memory bound.

base-depth become extremely slow when calculating highly covered site.

Thanks. I remember I also test with bed file input, and also wait for more than 20min. I will post my test results later.

base-depth become extremely slow when calculating highly covered site.

Seem that there is some problem with my previous test. I might forget to specify the bed file. I try to run the analysis with a bed file just now,...

[BUG] Snakemake fails to detect the correct path of config.yaml file when `executor` plugin is used.

The executor does not detect the workspace correctly and outputs all the files into the nested path. The output tree: ``` . ├── test │ └── test │ └── test.txt...