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peterjc / thapbi-pict

Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool
https://thapbi-pict.readthedocs.io/
MIT License
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Only apply abundance threshold in sample-tally #535

Closed peterjc closed 1 year ago

peterjc commented 1 year ago

This leaves the prepare-reads able to apply absolute and factional abundance, but the pipeline calls it with -a 2 and -f 0 to just drop singletons.

Could change the prepare-reads defaults too?

peterjc commented 1 year ago

Running into much higher memory usage on our full dataset in sample-tally when the input is not pre-abundance filtered. May be some easy fixes...

Update: e.g. https://github.com/peterjc/thapbi-pict/commit/9701b14862a0c3adeb314842fa5be78406b1aa5f

Update: Fixed in https://github.com/peterjc/thapbi-pict/commit/3b5dd79d3df8154347e688c7d7ea12ff72e0ac9a

peterjc commented 1 year ago

TODO: Rebase on top of #536