Commits for angie

f2b126d2fe65e705b4f6554f1c0c3b8dfb6d0a83 Wed May 31 12:37:39 2023 -0700

Check our reconstructed ancestral base value vs. the tree's par (parental/parsimonious?) base value.
- src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 10, context: html, text, full: html, text

aa32b124d6e43ec6717547bed2b18c489a1d04c8 Fri Jun 2 11:35:49 2023 -0700

If user uploads fasta with names that include characters with special meaning in Newick then replace those with _. Influenza sequence names often include serotype in parens e.g. (H3N2), (H5N6).
- src/hg/hgPhyloPlace/vcfFromFasta.c - lines changed 25, context: html, text, full: html, text

0c551e8432f5c9bbf86ac83e49a5c640ae7dbc55 Fri Jun 2 11:40:19 2023 -0700

Add support for a couple Influenza A RefSeq assemblies -- only for segment 4 (HA gene, the "H" in serotypes like "H3N2") for now since we'll need another menu (or smart matching) in order to support all segments.
- src/hg/hgPhyloPlace/hgPhyloPlace.c - lines changed 39, context: html, text, full: html, text
- src/hg/hgPhyloPlace/phyloPlace.c - lines changed 5, context: html, text, full: html, text
- src/hg/hgPhyloPlace/phyloPlaceMain.c - lines changed 18, context: html, text, full: html, text
- src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 24, context: html, text, full: html, text