[Suggestion] reducing messages to STDOUT to speed up the utility

[pacificbiosciences]

[Suggestion] reducing messages to STDOUT to speed up the utility

[holtjma]

Hello,

While this would reduce log clutter, it may also mask out legitimate errors in the underlying htslib crate/library that HiPhase is using. Currently, the errors from rust_htslib are passed through as warnings in this context, allowing users like yourself to identify issues with the input files that would be otherwise hidden without the warning. We could potentially add an option to disable the messages, but we would still leave these warnings on by default.

I wouldn't worry about run-time of the output, it is extremely insignificant relative to the rest of the phasing process.

Matt

p.s. glad HiPhase is working for you!

[davidyuyuan]

Thanks, Matt. An option to turn it off would be great.

[holtjma]

In the hundred of samples we've run internally, we haven't found anything significant that those messages were capturing that were not caught elsewhere in the code. As a result, we elected to just downgrade them to DEBUG level.

This should be resolved in v1.4.1, thanks for the suggestion!