Momoko NAGAI

CrossMap v0.5.4 outputs fake data when it failed to convert the data. $ `CrossMap.py vcf mm39ToMm10.over.chain.gz test.vcf mm10.fa out.vcf` - mm39ToMm10.over.chain.gz: `https://hgdownload.soe.ucsc.edu/goldenPath/mm39/liftOver/mm39ToMm10.over.chain.gz` - `test.vcf`, `out.vcf`, `out.vcf.unmap`: I attached it. [test.vcf.gz](https://github.com/liguowang/CrossMap/files/7114004/test.vcf.gz)...

B023: Why flake8 returns error only for a temporal variable for for loop?

8

flake8 causes error: `B023 Function definition does not bind loop variable 'chk_key'` for the following code. ``` ret_df = pd.DataFrame(index=target_df.index) for chk_key in [nalod, nlod]: ret_df[chk_key] = ( False if...

Why cannot docopt parse args?

3

python=3.10,6, docopt==0.6.2 [test.py] ``` #!/usr/bin/env python3 """ Usage: test.py [-h|--help] [-b|--bbbbb] (-r ) [-o ] [-l ...] options: -h,--help show this help message and exit -b,--bbbbb b option (optional) -r...

Does this issue occur when all extensions are disabled?: Yes/No - VS Code Version: 1.92.2 - OS Version: Windows 10 Pro 22H2 - Remote-SSH Version: v0.113.1 Steps to Reproduce: 1....

`make build` with ExomeDepth v1.1.18 or the latest code (at Sep. 29，2025) causes vignette error. I avoid this problem adding `--no-build-vignettes` to `R CMD build` in Makefile. Not urgent, but...