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CAMI-challenge / OPAL

OPAL: Open-community Profiling Assessment tooL
https://cami-challenge.github.io/OPAL/
Apache License 2.0
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Recover ability to set all internal branch lengths equal to 1, accounting for missing internal nodes #36

Open dkoslicki opened 4 years ago

dkoslicki commented 4 years ago

Due to changes in 428cd05, the old default of setting all branch lengths to 1 resulted in things like the following. For this profile:

# Taxonomic Profiling Output
@SampleID:CAMI_LOW_S001
@Version:0.9.1
@Ranks:superkingdom|phylum|class|order|family|genus|species|strain
@@TAXID RANK    TAXPATH TAXPATHSN   PERCENTAGE
<snip>
0   strain  5||||0  Viruses||||Viruses strain   10

if all internal branch lengths are 1, we should get a distance of 4 between nodes 5 and 0 (due to the missing internal ranks), but now after 428cd05, this will be set to:

and so a new option will need to be provided to recover the old behavior of setting all internal branch lengths to 1.