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fmicompbio / footprintR

Tools for working with single-molecule footprinting data
https://fmicompbio.github.io/footprintR/
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Add readModBam() to extract modification probabilities directly from bam files (MM/ML tags) #4

Closed mbstadler closed 3 months ago

mbstadler commented 3 months ago

I am opening this PR because it would be great to get your input on what you think about this.

The workhorse function read_modbam_cpp() is in C++ (so it will add a few dependencies) and seems to do what it needs, although I get a minority subset of probabilities that differ when comparing to the ones returned by modkit.

It would also be good to integrate filtering (at the moment, no filtering is performed, thus many more positions are returned than by modkit).

codecov-commenter commented 3 months ago

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mbstadler commented 3 months ago

I think that getReadDataForRegion() has become obsolete and superseded by readModBam(), which should do the same thing but more efficiently. If you agree, I'll remove it.