ff94dc36ad4584d7ccdeeb545b2b92825735d225
angie
  Fri Dec 8 09:55:19 2023 -0800
If an auspiceMeta.json file is specified in config.ra then use it for organism-specific tree colors & filters.  Also use CDS coords when writing genome annotations in Auspice output; not all viral genes are CDS-only.

diff --git src/hg/hgPhyloPlace/phyloPlace.h src/hg/hgPhyloPlace/phyloPlace.h
index 10baa28..ede0d8f2 100644
--- src/hg/hgPhyloPlace/phyloPlace.h
+++ src/hg/hgPhyloPlace/phyloPlace.h
@@ -146,30 +146,32 @@
     char *region;       // Continent on which sample was collected
     char *nCladeUsher;  // Nextstrain clade according to annotated tree
     char *lineageUsher; // Pango lineage according to annotated tree
     char *authors;      // Sequence submitters/authors
     char *pubs;         // PubMed ID numbers of publications associated with sequences
     char *nLineage;     // Nextstrain letter-dot-numbers lineage assigned by nextclade
     };
 
 struct geneInfo
 /* Information sufficient to determine whether a genome change causes a coding change. */
     {
     struct geneInfo *next;
     struct psl *psl;        // Alignment of transcript to genome
     struct dnaSeq *txSeq;   // Transcript sequence
     struct genbankCds *cds; // CDS (for those few pathogens that have transcript UTRs)
+    int cdsStart;           // genePred cdsStart (genome coord, really cds end if - strand)
+    int cdsEnd;             // genePred cdsEnd (genome coord, really cds start if - strand)
     };
 
 struct tempName *vcfFromFasta(struct lineFile *lf, char *db, struct dnaSeq *refGenome,
                               struct slName **maskSites, struct hash *treeNames,
                               struct slName **retSampleIds, struct seqInfo **retSeqInfo,
                               struct slPair **retFailedSeqs, struct slPair **retFailedPsls,
                               int *pStartTime);
 /* Read in FASTA from lf and make sure each item has a reasonable size and not too high
  * percentage of N's.  Align to reference, extract SNVs from alignment, and save as VCF
  * with sample genotype columns. */
 
 struct usherResults *runUsher(char *db, char *usherPath, char *usherAssignmentsPath, char *vcfFile,
                               int subtreeSize, struct slName **pUserSampleIds,
                               struct treeChoices *treeChoices, int *pStartTime);
 /* Open a pipe from Yatish Turakhia's usher program, save resulting big trees and