Mikko Rautiainen
Mikko Rautiainen
Thanks, fixed in 6bd39cb. There was an issue with minimizers sometimes reporting slightly wrong positions in the sequence, which caused the alignments to have extra indels. Let me know if...
The log seems to show it's commit c26721b which is not the latest. Could you try recompiling the latest commit of MBG (currently 10782bd) and rerunning with that? You might...
Hi, this is a bug. Could you share the input reads?
It's probably a different thing than issue 19. Could you upload the corrected hifi reads?
Yeah it seems to be pretty slow on that graph with `-x vg`. You can try these parameters instead: ``` --seeds-mxm-length 30 --seeds-mem-count 10000 --bandwidth 15 --multimap-score-fraction 0.99 --precise-clipping 0.85...
Using `--multimap-score-fraction 0` should prevent it from discarding alignments as secondary. If this doesn't work then could you upload a test graph and read where the secondary alignments are missing
@jarro2783 I was just going by the Boost implementation which doesn't change the help text for the parameter, but if you would like to add a help text that's fine...
Could you share the following files: ``` 4-processONT/normal-connected.gfa 4-processONT/fake-ont-nodecovs.csv 4-processONT/fake-ont-alns.gaf ```
Commit [7248729](https://github.com/marbl/verkko/commit/72487299dff0b56aedfc4600f31eed32a12fa1cf) in master branch should fix this bug