2aa99ff0ca7a50af99ba59a3e8a54d7a819e7808
angie
  Thu Aug 26 12:30:42 2021 -0700
Yikes, I was forgetting to expand condensed nodes in the big tree when making custom track VCF for subtrees, resulting in some sequences not being found & having no alt alleles in VCF.

diff --git src/hg/hgPhyloPlace/phyloPlace.h src/hg/hgPhyloPlace/phyloPlace.h
index 5c3de07..98f1a96 100644
--- src/hg/hgPhyloPlace/phyloPlace.h
+++ src/hg/hgPhyloPlace/phyloPlace.h
@@ -176,31 +176,31 @@
 
 struct slPair *getAaMutations(struct singleNucChange *sncList, 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, 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(struct tempName *vcfTn, struct usherResults *ur,
-                                   struct slName *sampleIds, struct phyloTree *bigTree,
+                                   struct slName *sampleIds, struct mutationAnnotatedTree *bigTree,
                                    char *source, int fontHeight, struct phyloTree **retSampleTree,
                                    int *pStartTime);
 /* Write one custom track per subtree, and one custom track with just the user's uploaded samples. */
 
 
 struct sampleMetadata *metadataForSample(struct hash *sampleMetadata, char *sampleId);
 /* Look up sampleId in sampleMetadata, by accession if sampleId seems to include an accession. */
 
 struct phyloTree *phyloPruneToIds(struct phyloTree *node, struct slName *sampleIds);
 /* Prune all descendants of node that have no leaf descendants in sampleIds. */
 
 char *phyloPlaceDbSetting(char *db, char *settingName);
 /* Return a setting from hgPhyloPlaceData/<db>/config.ra or NULL if not found. */
 
 char *phyloPlaceDbSettingPath(char *db, char *settingName);