Fix VCF parsing bugs #1924

Job	Run time
pathogen-repo-ci (avian-flu)	40s
test (python=3.8 biopython=1.76)	7m 3s
pathogen-repo-ci (ebola)	1m 1s
test (python=3.8 biopython=1.79)	7m 3s
pathogen-repo-ci (lassa)	44s
test (python=3.8 biopython=1.80)	7m 1s
pathogen-repo-ci (mumps)	1m 0s
test (python=3.8 biopython=latest)	7m 3s
pathogen-repo-ci (ncov)	1m 5s
test (python=3.9 biopython=1.79)	7m 7s
pathogen-repo-ci (seasonal-flu)	58s
test (python=3.9 biopython=1.80)	6m 57s
pathogen-repo-ci (tb)	1m 10s
test (python=3.9 biopython=latest)	7m 13s
pathogen-repo-ci (zika)	52s
test (python=3.10 biopython=1.80)	7m 13s
test (python=3.10 biopython=latest)	7m 9s
test (python=3.11 biopython=1.80)	7m 14s
test (python=3.11 biopython=latest)	7m 14s
build-docs / build-conda	0s
build-docs / build-pip	52s
codecov	0s
	1h 26m 39s

Provide feedback