Unable to change the default coverage parameter for naive LCA assignment with malt v. 0.4.1

Dear developers,

Following the issue I encountered with malt v. 0.5.* (which is described here: LCA placement failure with Malt v. 0.5.2 and 0.5.3), I tried to switch back to v. 0.4.1.

I encountered a different issue with this version, which is the following:

By default, the LCA placement appears to be made with a “naive algorithm” and 80% “coverage”, as stated by the malt-run log:

Using 'Naive LCA' algorithm (80.0 %) for binning: Taxonomy

If I understand correctly (also from some testing that I have done), this means that if more than 80% of the references that are hit by a read belong to the same taxon, the read will be assigned to that taxon, ignoring the other references that might have been hit. For example, if there are 8 references for Yersinia pestis and only 2 references for Yersinia pseudotuberculosis in the index, a read hitting all of these will be assigned to Y. pestis (even if the hit to Y. pseudotuberculosis is the best hit).

As for the previous issue, I could not find a way to change this behaviour using available commandline options.

I think that this can be problematic for people using customized reference datasets that are uneven. Typically, for datasets comprising many references for target taxa and just a few “outgroups”, unspecific matches might be reported as specific matches to target taxa.

I just tested this, appears to work correctly in the new release, but please let me know if there are still problems.

Actually, please update to version 0.6.1, were the bug has finally been squashed

Everything seems to work fine with v. 0.6.1, thanks Daniel!