filter: Split filtering and subsampling #2217

Job	Run time
pathogen-repo-ci (avian-flu)	1m 19s
test (python=3.8 biopython=1.80)	3m 24s
pathogen-repo-ci (ebola)	3m 47s
test (python=3.8 biopython=latest)	3m 34s
pathogen-repo-ci (lassa)	1m 22s
test (python=3.9 biopython=1.80)	3m 38s
pathogen-repo-ci (mumps)	1m 31s
test (python=3.9 biopython=latest)	3m 40s
pathogen-repo-ci (ncov)	1m 34s
test (python=3.10 biopython=1.80)	3m 37s
pathogen-repo-ci (rsv)	2m 51s
test (python=3.10 biopython=latest)	3m 34s
pathogen-repo-ci (seasonal-flu)	1m 44s
test (python=3.11 biopython=1.80)	3m 38s
pathogen-repo-ci (tb)	1m 56s
test (python=3.11 biopython=latest)	3m 32s
build-docs / build-pip	54s
build-docs / build-conda	0s
codecov	0s
	45m 35s

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