Open davidnewman02 opened 5 months ago
This is probably caused by the same bug #1177 and/or #1181. I will cut a new release later this week.
I am able to reproduce this bug in earlier mappy versions (tested back to 2.18), so I think this might be a different root cause as those issues appear to be due to more recent code additions.
EDIT: I have just downloaded the latest mappy=2.28
and can confirm the Segfault is still present for this read.
I have a very long read (~500kb) which I try to align using
mappy
in python using theMD=True
flag and this gives a Segfault. This read does not align well, with a large amount of soft-clipping.This does not appear to happen with the
minimap2
standalone executable or whenMD=False
read.fastq.txt NB The full reference file is too large for a gitlab issue, but is T2T-v1.0 with a small amount of local cleanup: https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/HG002/assemblies/hg002v1.0.fasta
output:
The equivalent with standalone minimap2 runs successfully: