4dc2ce3ec067b4ccb7987cbda16289d165954971
angie
  Thu Mar 9 20:04:39 2023 -0800
Translate multiple changes to the same codon correctly, collecting all mutations on the path from root to node.

diff --git src/hg/hgPhyloPlace/phyloPlace.h src/hg/hgPhyloPlace/phyloPlace.h
index 1fc9fc8..da9ea20 100644
--- src/hg/hgPhyloPlace/phyloPlace.h
+++ src/hg/hgPhyloPlace/phyloPlace.h
@@ -188,32 +188,32 @@
 boolean startServer(char *db, struct treeChoices *treeChoices, FILE *errFile);
 /* Start up an usher-sampled-server process to run in the background. */
 
 void serverReloadProtobufs(char *db, struct treeChoices *treeChoices);
 /* Send a reload command and list of protobufs for db to usher server. */
 
 void serverStop(char *db);
 /* Send stop command to usher server. */
 
 void serverSetThreadCount(char *db, int val);
 /* Send thread command and value to usher server. */
 
 void serverSetTimeout(char *db, int val);
 /* Send timeout command and value (in seconds) to usher server. */
 
-struct slPair *getAaMutations(struct singleNucChange *sncList, struct geneInfo *geneInfoList,
-                              struct seqWindow *gSeqWin);
+struct slPair *getAaMutations(struct singleNucChange *sncList, struct singleNucChange *ancestorMuts,
+                              struct geneInfo *geneInfoList, struct seqWindow *gSeqWin);
 /* Given lists of SNVs and genes, return a list of pairs of { gene name, AA change list }. */
 
 struct geneInfo *getGeneInfoList(char *bigGenePredFile, struct dnaSeq *refGenome);
 /* If config.ra has a source of gene annotations, then return the gene list. */
 
 void treeToAuspiceJson(struct subtreeInfo *sti, char *db, struct geneInfo *geneInfoList,
                        struct seqWindow *gSeqWin, struct hash *sampleMetadata,
                        struct hash *sampleUrls, struct hash *samplePlacements,
                        char *jsonFile, char *source);
 /* Write JSON for tree in Nextstrain's Augur/Auspice V2 JSON format
  * (https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v2.json). */
 
 struct tempName *writeCustomTracks(char *db, struct tempName *vcfTn, struct usherResults *ur,
                                    struct slName *sampleIds, char *source, int fontHeight,
                                    struct phyloTree **retSampleTree, int *pStartTime);