Support HDF5 outputs again

PacificBiosciences / kineticsTools

Tools for detecting DNA modifications from single molecule, real-time sequencing data

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Support HDF5 outputs again #89

Open hisakatha opened 2 years ago

hisakatha commented 2 years ago

Hello,

I noticed that the HDF5 output (--csv_h5) option in ipdSummary was removed at d5675a4efe03167d03d93864368067d1f99f34ae, but I could not find related discussion. I would like ipdSummary to support the HDF5 output again, if there are no problems.

In addition, I would like the SMRT Tools manual to be consistent with the implementation, since it still refers to the --csv_h5 option (p. 48).

natechols commented 2 years ago

Sorry, h5py is a difficult dependency to maintain, and that particular feature was ultimately more trouble to run than it was worth. If you want to use it anyway, you could check out the smrtlink-5.0.0 branch: https://github.com/PacificBiosciences/kineticsTools/tree/smrtlink-5.0.0 But thank you for pointing out the documentation error, I will get that fixed.