17cdc50389b482ee9f3f1ce649ed297201269d53
angie
  Thu Feb 25 20:41:01 2021 -0800
If usher's output includes clade and lineage assignments, parse them and include them in the summary table.

diff --git src/hg/hgPhyloPlace/phyloPlace.h src/hg/hgPhyloPlace/phyloPlace.h
index 74969b3..9fc1f0c 100644
--- src/hg/hgPhyloPlace/phyloPlace.h
+++ src/hg/hgPhyloPlace/phyloPlace.h
@@ -73,30 +73,32 @@
     struct baseVal *next;
     int chromStart;         // 0-based position
     char *val;              // nucleotide base(s)
     };
 
 struct placementInfo
 /* Info about a sample's mutations and placement in the phylo tree */
     {
     char *sampleId;                       // Sample name from FASTA or VCF header
     struct slName *sampleMuts;            // Differences with the reference genome
     struct variantPathNode *variantPath;  // Mutations assigned to nodes along path from root
     struct bestNodeInfo *bestNodes;       // Other nodes identified as equally parsimonious
     struct baseVal *imputedBases;         // Ambiguous bases imputed to ref/alt [ACGT]
     int parsimonyScore;                   // Parsimony cost of placing sample
     int bestNodeCount;                    // Number of equally parsimonious placements
+    char *nextClade;                      // Nextstrain clade assigned by UShER
+    char *pangoLineage;                   // Pango lineage assigned by UShER
     };
 
 struct subtreeInfo
 /* Parsed subtree from usher and derivative products. */
     {
     struct subtreeInfo *next;
     struct tempName *subtreeTn;           // Newick file from usher (may have condensed nodes)
     struct phyloTree *subtree;            // Parsed subtree (#*** with annotated muts?  shoudl we?_
     struct hash *subtreeIdToIx;           // Map of subtree nodes to VCF output sample order
     struct slName *subtreeUserSampleIds;  // List of user-uploaded samples in this subtree
     struct slName *subtreeNameList;       // List of leaf names with nicer names for cond. nodes
     };
 
 struct usherResults
 /* Tree+samples download file, sample placements, and subtrees parsed from usher output. */