Update species probes #177
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This reverts commit 72e0b74.
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This reverts commit 8ecab6f.
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This reverts commit 72e0b74.
This reverts commit 676a656.
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Windows build is breaking because the install of numpy is broken and causing myrkobe to throw import/library not found errors. Making separate issue for that. Merging now because we want a new release ASAP. The release will be without Windows. |
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The tb species probes are going to be updated after the next release of
mykrobe. Code changed to handle these new probes, specifically where a node in
the taxon tree has no probes. If a child node is called as present from the
reads, then push that call up to the parent node. Code still works as normal
on the existing (soon to be old) panels.
Added flag
--ncbi_names. This is for soon to be updated tb probes forspecies calling, where the JSON file will also report alternative NCBI taxon
names, as well as the default GTBD names.
Added option
--dump_species_covgs, to dump a JSON file of all the speciesprobe coverage information. This includes the raw coverage info from mccortex,
before it is aggregated into a single call that you see in the usual
mykrobe output
Also ran black, so a bunch of changes are just cosmetic