Feat: HMMRATAC integration

[taoliu]

HMMRATAC (https://github.com/LiuLabUB/HMMRATAC) is a dedicated peak caller for ATAC-seq data. It is written in JAVA, and it has some shared ideas with MACS2. It can be rewritten in Python3 and be integrated into MACS as a subcommand while dealing with ATAC-seq data.

Describe the solution you'd like

1. JAVA -> Python3 translation
2. Share MACS components
3. Design unit tests

Additional context
Some difficulties: HMMRATAC contains machine learning components such as EM algorithm, and Hidden Markov Models. We may need to introduce more dependencies including scikit-learn, hmmlearn and matplotlib.

[hyjforesight]

Hello @taoliu,
just want to check whether it is available to call HMMRATAC in MACS3 now? I didn't find this sub function in MACS3.

Thanks!
Best,
YJ

[taoliu]

@hyjforesight We are developing it in this branch: https://github.com/macs3-project/MACS/tree/feat/macs3/hmmratac Almost there :)