This is a minor issue. It can be described as inferring a VCF ref from a PRG, and then using this VCF ref for subsequent pandora map/compare, and pandora complaining that it does not match the PRG, e.g.:
[2023-01-14 13:04:25.770326] [0x0000145b453cd700] [warning] Input vcf_ref path did not start/end at the beginning/end of PRG CP050286.1_00072.fa.msa
[2023-01-14 13:06:17.166907] [0x0000145b4e711700] [warning] Input vcf_ref path did not start/end at the beginning/end of PRG CP033559.1_00077.fa.msa
[2023-01-14 13:06:22.984843] [0x0000145b4e30f700] [warning] Input vcf_ref path did not start/end at the beginning/end of PRG NZ_CP042833.1_00216.fa.msa
This is happening in roundhound (see https://github.com/LeahRoberts/roundhound/issues/86), but is a minor issue because it just affects 3 genes. I suspect this might be related with a deletion at the start of the first site, but might be wrong. As it is minor, we decided not to fix this right now. However, data to reproduce this follows:
This is a minor issue. It can be described as inferring a VCF ref from a PRG, and then using this VCF ref for subsequent
pandora map/compare
, andpandora
complaining that it does not match the PRG, e.g.:This is happening in roundhound (see https://github.com/LeahRoberts/roundhound/issues/86), but is a minor issue because it just affects 3 genes. I suspect this might be related with a deletion at the start of the first site, but might be wrong. As it is minor, we decided not to fix this right now. However, data to reproduce this follows:
VCF ref:
PRG:
MSA