Expand cattle-outbreak beyond B3.13

[jameshadfield]

With the recent move to B3.13 filtering defining the cattle-outbreak genome build we are not able to include strains with fewer than 8 sequenced segments (and thus the implementation in #111 is outdated). Furthermore we're going to drop some strains because their genoFLU calls aren't B3.13. Comparing the last successful cattle-flu dataset we are going to drop the following strains due to not being B3.13:

$ cat data/ncbi/metadata.tsv | csvtk grep -t -f strain -P auspice.strains.tsv | csvtk cut -t -f strain,genoflu | grep -v B3.13 | csvtk pretty -t
strain                                  genoflu                                                                           
-------------------------------------   ----------------------------------------------------------------------------------
A/cattle/Texas/24-009499-002/2024       Not assigned: No Matching Genotypes                                               
A/cattle/Texas/24-009308-003/2024       Not assigned: Only 7 segments >98.0% match found of total 8 segments in input file
A/cattle/NewMexico/24-010195-004/2024   Not assigned: Only 7 segments >98.0% match found of total 8 segments in input file
A/cattle/Colorado/Broad_MD_041/2024     Not assigned: Only 6 segments >98.0% match found of total 8 segments in input file
A/cattle/Colorado/Broad_ME_003/2024     Not assigned: Only 6 segments >98.0% match found of total 8 segments in input file
A/cattle/Idaho/Broad_ME_018/2024        Not assigned: Only 6 segments >98.0% match found of total 8 segments in input file
A/cattle/Idaho/Broad_ME_020/2024        Not assigned: Only 7 segments >98.0% match found of total 8 segments in input file
A/cattle/Colorado/Broad_MF_011/2024     Not assigned: Only 5 segments >98.0% match found of total 8 segments in input file
A/cattle/Missouri/Broad_MD_031/2024     Not assigned: Only 7 segments >98.0% match found of total 8 segments in input file
A/cattle/Texas/Broad_MD_027/2024        Not assigned: Only 5 segments >98.0% match found of total 8 segments in input file
A/cattle/Colorado/Broad_MF_016/2024     Not assigned: Only 6 segments >98.0% match found of total 8 segments in input file
A/cattle/Michigan/Broad_ME_010/2024     Not assigned: Only 7 segments >98.0% match found of total 8 segments in input file
A/Cattle/USA/24-031346-001/2024         Not assigned: Only 7 segments >98.0% match found of total 8 segments in input file
A/Cattle/USA/24-032636-001/2024         Not assigned: Only 7 segments >98.0% match found of total 8 segments in input file
A/Cattle/USA/24-034010-002/2024         Not assigned: Only 7 segments >98.0% match found of total 8 segments in input file
A/Cattle/USA/24-034010-001/2024         Not assigned: Only 7 segments >98.0% match found of total 8 segments in input file
A/Cattle/USA/24-033997-001/2024         Not assigned: Only 7 segments >98.0% match found of total 8 segments in input file
A/PETFOOD/USA/24-037325-013/2024        Not assigned: Only 7 segments >98.0% match found of total 8 segments in input file
A/PETFOOD/USA/24-037325-012/2024        Not assigned: Only 5 segments >98.0% match found of total 8 segments in input file

Including full genome strains which don't match B3.13

We may wish to relax the 98% cutoff. Looking at some of those examples above the number of Ns is perhaps behind their exclusion:

• A/cattle/Texas/24-009499-002/2024 has 4.5kb of Ns on the branch leading to it, although few mutations indicating that it is likely to be part of the outbreak
• A/cattle/Texas/24-009308-003/2024 - similarly - 4.5kb of Ns

Including strains with fewer than 8 segments sequenced

If we modify GenoFLU to report segment-level calls for strains with <8 segments then we can match on (e.g) "7 segments sequenced and all agree with B3.13 constellation". This improvement to GenoFLU was also mentioned here as being desirable more generally.