vg call-c and -C options changed to limit search based on all alleles and not just reference allele. This means these options work much better in practice to prevent vg call from being lost in giant snarls.
--progress option added to vg call
Description
It's come up a number of times where people try to run vg call on complex graphs and runs forever. The reason being is that it gets lost trying to find traversals through enormous snarls, and there is not enough signal in the read mappings to narrow the search down to something manageable. The min/max traversal cutoffs -c/-C were added to address this, but since they only filtered on reference allele length, they only helped sometimes -- it just takes a giant insertion to get around this. This PR changes these options to take into account alt alleles as well. So if you run -c 50 -c 1000, it will only try to genotype sites where at least one traversal is >=50bp, and it will give up on any site as soon as a single traversal >1000bp is found.
Changelog Entry
To be copied to the draft changelog by merger:
vg call-cand-Coptions changed to limit search based on all alleles and not just reference allele. This means these options work much better in practice to preventvg callfrom being lost in giant snarls.--progressoption added tovg callDescription
It's come up a number of times where people try to run
vg callon complex graphs and runs forever. The reason being is that it gets lost trying to find traversals through enormous snarls, and there is not enough signal in the read mappings to narrow the search down to something manageable. The min/max traversal cutoffs-c/-Cwere added to address this, but since they only filtered on reference allele length, they only helped sometimes -- it just takes a giant insertion to get around this. This PR changes these options to take into account alt alleles as well. So if you run-c 50 -c 1000, it will only try to genotype sites where at least one traversal is>=50bp, and it will give up on any site as soon as a single traversal>1000bpis found.