DRB1-3123 example not producing a nice graph anymore after biwflambda update.

[subwaystation]

Using the Dockerfile from #231 I get quite an ugly DRB1-3123 graph:

docker pull ghcr.io/pangenome/pggb:latest
docker run -it -v ${PWD}/data/:/data ghcr.io/pangenome/pggb:latest "pggb -i /data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 2000 -n 12 -t 16 -o /data/bi_wfmash_test -M -m"

[ekg]

What happens with default parameters?

[subwaystation]

docker run -it -v ${PWD}/data/:/data ghcr.io/pangenome/pggb:latest "pggb -i /data/HLA/DRB1-3123.fa.gz -n 12 -t 16 -o /data/bi_wfmash_test_1 -M -m

Other fancy graphs.

[subwaystation]

Alright, I got a nice one with this:

docker run -it -v ${PWD}/data/:/data ghcr.io/pangenome/pggb:latest "pggb -i /data/HLA/DRB1-3123.fa.gz -p 70 -s 2000 -G 2000 -n 12 -t 16 -o /data/bi_wfmash_test_2 -M -m"

A shorter segment length was required. I am happy now.

[ekg]

I'd suggest removing -G... that part is very different now. We actually iterate with very short -G three times. So we're just doing very local smoorthing now.

[subwaystation]

Not sure this helped. The tip of the cavallo seems worse.