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zengxiaofei / HapHiC

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data
https://www.nature.com/articles/s41477-024-01755-3
BSD 3-Clause "New" or "Revised" License
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BED file support #26

Open amvarani opened 6 months ago

amvarani commented 6 months ago

Hi there Is it possible to implement support for BED files along with BAM and PAIR formats?

Best regards

zengxiaofei commented 6 months ago

Hi @amvarani,

As far as I know, SALSA is currently the only tool that utilizes BED files. There is no widely used aligner for Hi-C/Pore-C data that outputs alignments in BED format. Additionally, the BED files input into SALSA are converted from BAM files. Therefore, we currently do not have the plan to provide support for BED files. Sorry!

Best, Xiaofei

amvarani commented 6 months ago

Hello @zengxiaofei

Thank you for the quick response. I appreciate the information provided.

I'd like to share that other programs, such as YAHS, also utilize the BED format. Additionally, one advantage that BED files have over BAM files is their significantly smaller size, which makes them more efficient for data storage and management. From an infrastructure perspective, adopting BED files could offer a notable advantage when managing large datasets.

Furthermore, because BED files are text-based, they are easier to manipulate and inspect compared to the more complex BAM format. Their versatility and ease of use make them beneficial for quick data exploration and downstream analyses.

I hope this additional perspective might be useful as you consider future developments.

Best wishes and really thanks for the development of this excellent tool HapHic! :)

zengxiaofei commented 6 months ago

Thank you for sharing this valuable information. You have convinced me, and I will make this update when I have time. Best wishes!