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PacificBiosciences / pb-CpG-tools

Collection of tools for the analysis of CpG data
BSD 3-Clause Clear License
70 stars 6 forks source link

Can I use CpG tools if I have other basemods in the file #48

Closed mrvollger closed 1 year ago

mrvollger commented 1 year ago

Hi @ctsa,

I think the answer is going to be no based on a phrase in the docs but can I use CpG tools if I have other basemods in addition to CpG in the MM and ML tags?

Thanks! Mitchell

ctsa commented 1 year ago

Hi @mrvollge - It's possible we could support this if we had some way to verify correctness, and parse the two modifications serially instead of the multi-modification format also described in the spec. I'll followup with you for details.

ctsa commented 1 year ago

I checked the parser code tests and completed a test on a bam file with other basemods besides 5mC. It looks like this capability is already supported and works correctly. I'll update the README to reflect this. Please reopen this ticket if you run into problems.