WIP: reduce minimizer threshold from 0.3 to 0.1 #1409
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The sort command currently outputs a sequence into a file corresponding to the dataset prefix if a dataset with this prefix is a hit. If we changed this to the more stringent condition that the dataset needs to be the best hit, the sort would work more as a hierarchical sort. |
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If I understand this correctly, one could only process the first (best) dataset here: |
This allows to unambiguously and reliably map entries in the input fasta to the entries in the output tsv, which is important in presence of duplicated sequence names.
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for very diverse viruses, our current match fraction threshold of 0.3 for minimizers is too stringent. 0.1 is still very sensitive in the sense that no random hits are produced. But we have many suboptimal hits between related viruses. (like RSV-A matching RSV-B). This is not a problem as long as we consider the best hit. But in the
sortcommand we end up not sorting anymore.