Feat: Enhanced clarification of the specific definition of BEDPE as used by MACS

[kalavattam]

Intro
Hi @taoliu,

First, I want to express my gratitude for your dedication to developing and maintaining such a valuable tool as MACS. It's been instrumental in advancing our research.

Is your feature request related to a problem? Please describe.
I recently encountered a bit of confusion regarding the terminology used for BED output from paired-end sequencing data. Specifically, the term "BEDPE" seems to conflict with an already established format closely associated with Hi-C data, as detailed here.

For example, during my use of macs3 filterdup, I anticipated an output in the above-defined BEDPE format but received a three-column BED-like file instead. This discrepancy wasn't immediately clear from the macs3 filterdup documentation. Upon following the suggestion in the documentation,

-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}, --format {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}
                        Format of tag file, "AUTO", "BED" or "ELAND" or "ELANDMULTI" or "ELANDEXPORT" or "SAM" or "BAM" or "BOWTIE" or "BAMPE" or "BEDPE". The default AUTO option will let 'macs3 filterdup' decide which format the file is. Please check the definition in README file if you choose ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE or BAMPE/BEDPE. DEFAULT: "AUTO"

...I didn't find a specific definition of BEDPE as used by MACS in the README Markdown file. I did, however, find it in the repo's callpeak Markdown file.

Describe the solution you'd like
For clarity and to help future users, it might be beneficial to explicitly define the BEDPE format as understood by MACS, possibly in the main README or within the tool's documentation text for macs3 filterdup and the various other functions. This small adjustment could enhance user experience and prevent similar confusion.

Describe alternatives you've considered
Alternatively, it might be good to explicitly refer to callpeak.md, instead of the term "README file", in the help documentation for the various functions.

Outro
Thank you again for your incredible work on this project. Your efforts are greatly appreciated by the scientific community.

Best,
Kris

[taoliu]

@kalavattam Thanks for your suggestion! We should write a dedicated document regarding the various formats of input and output files. I just managed to use Sphinx to build a better documentation site: https://macs3-project.github.io/MACS/