How about to change circle-map to C++ version?

nf-core / circdna

Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.

https://nf-co.re/circdna

MIT License

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How about to change circle-map to C++ version? #66

Open panxiaoguang opened 5 months ago

panxiaoguang commented 5 months ago

Description of feature

The original version of Circle-Map is a little bit slow, especially when it processes reads that contain a high percentage of ChrM. The C++ reimplementation of Circle-Map can deal with this situation and will be a faster alternative. Thus, It would be a good idea to use C++ version in the pipeline.

panxiaoguang commented 5 months ago

please find it in https://github.com/BGI-Qingdao/Circle-Map-cpp

DSchreyer commented 5 months ago

I agree. Can you try to make a pull request to dev for this ? I might be able to include it then into the newest version 1.1