eeac40956b3dd6611f58aeb847ff5c404d3ce883
angie
  Fri Dec 1 09:05:41 2023 -0800
Support trees whose reference/root is not from a db or hub, but rather a custom .2bit file.
This means that the selected pathogen may or may not also be a db/hub, so the selection interacts with the db cart variable but does not always match it.
Also, in phyloPlace.c, update RSV metadata column headers (RGCC lineages replace Ramaekers 2020 clades).

diff --git src/hg/hgPhyloPlace/phyloPlaceMain.c src/hg/hgPhyloPlace/phyloPlaceMain.c
index 07b51be..bcbbc19 100644
--- src/hg/hgPhyloPlace/phyloPlaceMain.c
+++ src/hg/hgPhyloPlace/phyloPlaceMain.c
@@ -49,22 +49,22 @@
 boolean success = FALSE;
 
 int timeout = 300;
 if (udcCacheTimeout() < timeout)
     udcSetCacheTimeout(timeout);
 knetUdcInstall();
 
 if (isHubTrack(db))
     {
     // Connect to hubs so phyloPlaceSamples doesn't croak later.
     struct cart *cart = cartOfNothing();
     struct slName *supportedDbs = phyloPlaceDbList(cart);
     if (! slNameInList(supportedDbs, db))
         errAbort("Can't find db '%s'", db);
     }
-char *ctFile = phyloPlaceSamples(lf, db, protobuf, TRUE, subtreeSize, 9, &success);
+char *ctFile = phyloPlaceSamples(lf, "hg38", db, protobuf, TRUE, subtreeSize, 9, &success);
 if (ctFile)
     printf("ctFile = %s\n", ctFile);
 else
     printf("no ctFile.\n");
 return (success == TRUE);
 }