705420e703b067fbcad43ab67ed3e131552e7ac8
angie
  Wed Apr 24 14:23:03 2024 -0700
Pathogen drop-down choices can now be groups of references/trees, for example 'Dengue (types 1 - 4)' instead of a separate choice for each type.
Instead of config.ra, each group has an organism.ra and subdirectories named after reference accessions that contain reference.ra files.
nextclade sort is used to match the user's uploaded sequences against available references for the selected pathogen.
SARS-CoV-2, M. tuberculosis and hMPXV still have only one reference and still use config.ra, but RSV, Dengue and Influenza will become groups.
Presentation is still kinda rough, just a loop on the original results output.
The server commands part needs testing and will not work yet for groups (currently used only for SARS-CoV-2).

diff --git src/hg/hgPhyloPlace/writeCustomTracks.c src/hg/hgPhyloPlace/writeCustomTracks.c
index b27841a..0293f6d 100644
--- src/hg/hgPhyloPlace/writeCustomTracks.c
+++ src/hg/hgPhyloPlace/writeCustomTracks.c
@@ -1,18 +1,18 @@
 /* Write custom tracks: one per subtree and one with user's uploaded samples. */
 
-/* Copyright (C) 2020 The Regents of the University of California */
+/* Copyright (C) 2020-2024 The Regents of the University of California */
 
 #include "common.h"
 #include "hash.h"
 #include "hdb.h"
 #include "iupac.h"
 #include "parsimonyProto.h"
 #include "phyloPlace.h"
 #include "phyloTree.h"
 #include "trashDir.h"
 #include "vcf.h"
 
 static char ***imputedBasesByPosition(struct hash *samplePlacements, struct slName *sampleIds,
                                       int chromSize)
 /* Unpack imputedBases into an array of (a few) arrays indexed by 0-based position and sample index,
  * for speedy retrieval while rewriting user VCF. */
@@ -510,38 +510,39 @@
     return;
     }
 struct subtreeInfo *ti;
 int subtreeNum;
 for (subtreeNum = 1, ti = subtreeInfoList;  ti != NULL;  ti = ti->next, subtreeNum++)
     {
     writeSubtreeTrackLine(ctF, ti, subtreeNum, source, geneTrack, fontHeight);
     writeVcfHeader(ctF, ti->subtreeNameList);
     writeSubtreeVcf(ctF, ti->subtreeIdToIx, chrom, chromSize, userVcf, ti->subtree);
     fputc('\n', ctF);
     }
 vcfFileFree(&userVcf);
 reportTiming(pStartTime, "write subtree custom tracks");
 }
 
-struct tempName *writeCustomTracks(char *db, struct tempName *vcfTn, struct usherResults *ur,
+struct tempName *writeCustomTracks(char *org, char *ref, char *db,
+                                   struct tempName *vcfTn, struct usherResults *ur,
                                    struct slName *sampleIds, char *source, int fontHeight,
                                    struct phyloTree *sampleTree, int *pStartTime)
 /* Write one custom track per subtree, and one custom track with just the user's uploaded samples. */
 {
 char *chrom = hDefaultChrom(db);
 int chromSize = hChromSize(db, chrom);
-char *geneTrack = phyloPlaceDbSetting(db, "geneTrack");
+char *geneTrack = phyloPlaceRefSetting(org, ref, "geneTrack");
 // Default to SARS-CoV-2 or hMPXV values if setting is missing from config.ra.
 if (isEmpty(geneTrack))
     geneTrack = sameString(db, "wuhCor1") ? "ncbiGeneBGP" : "ncbiGene";
 struct tempName *ctVcfTn = userVcfWithImputedBases(vcfTn, ur->samplePlacements, sampleIds,
                                                    chromSize, pStartTime);
 struct tempName *ctTn;
 AllocVar(ctTn);
 trashDirFile(ctTn, "ct", "ct_pp", ".ct");
 FILE *ctF = mustOpen(ctTn->forCgi, "w");
 int subtreeCount = slCount(ur->subtreeInfoList);
 if (subtreeCount <= MAX_SUBTREE_CTS)
     addSubtreeCustomTracks(ctF, ctVcfTn->forCgi, ur->subtreeInfoList, ur->samplePlacements,
                            chrom, chromSize, source, geneTrack, fontHeight, pStartTime);
 else
     printf("<p>Subtree custom tracks are added when there are at most %d subtrees, "