Updated H3N2 reference to A/Perth/16/2009.

[cassiawag]

This commit should address #9 & #10. I swapped out all reference genomes for H3N2 for A/Perth/16/2009 segments, and I also updated the script create_ref_genome.py to add header information for reference_{lineage}_genome.gb.

[trvrb]

@cassiawag: Thank you! Can you rebase these onto two separate PRs? Best practice is to have PRs be issue-specific.

[cassiawag]

Done! This PR now only updates the reference sequences in the config folder; should fix #10
@trvrb

[cassiawag]

In Snakefile, just updated def reference_strain(wildcards): to specify A/Perth/16/2009 for H3N2.

[trvrb]

@cassiawag: Thanks for putting in this PR. I now believe that A/Beijing/32/1992 is working well as a reference strain. I realize now moving to A/Perth/16/2009 will require updating

• https://github.com/seattleflu/augur-build/blob/master/config/clades_h3n2_ha.tsv
• https://github.com/seattleflu/augur-build/blob/master/config/exclude-sites_h3n2_genome.txt
• https://github.com/seattleflu/augur-build/blob/master/config/ha_masks.tsv
  Better to wait on this. I'm going to close this PR, but let's keep the ref_genome branch around.