Indels currently don't match by alleles (I think) and are skipped.
Trying to debug this is weird. Print statements don't appear to be working for some bizarre reason.
Also, it appears that there is some strange behavior with looping over the filtering list. I think some pieces need to be moved outside of the loop. For example, if multiple variants are in the filter list, but the first variant fails (e.g. if it's an indel currently) then the loop seems to break and the rest of the variants are skipped for that sample.
Indels currently don't match by alleles (I think) and are skipped.
Trying to debug this is weird. Print statements don't appear to be working for some bizarre reason.
Also, it appears that there is some strange behavior with looping over the filtering list. I think some pieces need to be moved outside of the loop. For example, if multiple variants are in the filter list, but the first variant fails (e.g. if it's an indel currently) then the loop seems to break and the rest of the variants are skipped for that sample.