bug? hit.c:210: mm_hit_sort: Assertion `has_cigar + no_cigar == 1' failed.

[dgordon562]

I've been seeing this quite a bit lately. It happens with ONT reads with these parameters:
-t 10 -a -x map-ont --secondary=no --split-prefix $TMPDIR/ -N 100

I've also seen it aligning hifi reads with these parameters:
-t 10 -a -r 2k -Y -x map-pb -O 5,56 -E 4,1 -B 5 -z 400,50 --split-prefix $TMPDIR/ -N 100 -p 0.01 -m 1000

The datasets that reproduce this error are huge. If there is interest, I can work on creating a smaller dataset that reproduces this error.

[BIGtigr]

How did you fix this issue? I met the same problem

[RPHdeJongh-naktuinbouw]

I also have this problem with the following settings. Very large database and large set of ONT-reads.

settings here are: -a -x map-ont -y -t 60 --split-prefix tmp_minimap

[lh3]

This is probably specific to --split-prefix, which is rarely used. If you can find a small dataset to reproduce the issue, I may have a look in future.