1ab96609fb58d6c6053425989043e9e7c5dd9f99
angie
  Mon Jan 10 08:56:42 2022 -0800
Update Nextstrain clade names and color spectrum in Auspice JSON output.

diff --git src/hg/hgPhyloPlace/treeToAuspiceJson.c src/hg/hgPhyloPlace/treeToAuspiceJson.c
index f704622..02e6bed 100644
--- src/hg/hgPhyloPlace/treeToAuspiceJson.c
+++ src/hg/hgPhyloPlace/treeToAuspiceJson.c
@@ -27,77 +27,77 @@
 if (sampleCount > 10)
     fprintf(outF, " and %d other uploaded samples", sampleCount - 1);
 else
     {
     struct slName *sln;
     for (sln = subtreeUserSampleIds->next;  sln != NULL;  sln = sln->next)
         fprintf(outF, ", %s", sln->name);
     }
 fputs("\", "
       "\"panels\": [ \"tree\"] , "
       "\"colorings\": [ "
       "  { \"key\": \"pango_lineage\", "
       "    \"title\": \"Pango lineage\", \"type\": \"categorical\" },"
       "  { \"key\": \"Nextstrain_clade\","
       "    \"scale\": [ "
-      "        [ \"20H (Beta, V2)\", \"#3F47C9\" ],"
-      "        [ \"20I (Alpha, V1)\", \"#4274CE\" ],"
-      "        [ \"20J (Gamma, V3)\", \"#4F97BB\" ],"
-      "        [ \"21A (Delta)\", \"#64AC99\" ],"
-      "        [ \"21B (Kappa)\", \"#7EB976\" ],"
-      "        [ \"21C (Epsilon)\", \"#9EBE5A\" ],"
-      "        [ \"21D (Eta)\", \"#BEBB48\" ],"
-      "        [ \"21E (Theta)\", \"#D9AE3E\" ],"
-      "        [ \"21F (Iota)\", \"#E69036\" ],"
-      "        [ \"21G (Lambda)\", \"#E35F2D\" ],"
-      "        [ \"21H\", \"#DB2823\" ],"
+      "        [ \"20H (Beta, V2)\", \"#571EA2\" ],"
+      "        [ \"20I (Alpha, V1)\", \"#4334BF\" ],"
+      "        [ \"20J (Gamma, V3)\", \"#3F55CE\" ],"
+      "        [ \"21A (Delta)\", \"#4376CD\" ],"
+      "        [ \"21I (Delta)\", \"#4C91C0\" ],"
+      "        [ \"21J (Delta)\", \"#59A4A9\" ],"
+      "        [ \"21C (Epsilon)\", \"#7FB975\" ],"
+      "        [ \"21D (Eta)\", \"#97BD5F\" ],"
+      "        [ \"21F (Iota)\", \"#C7B944\" ],"
+      "        [ \"21G (Lambda)\", \"#D9AD3D\" ],"
+      "        [ \"21H (Mu)\", \"#E49838\" ],"
+      "        [ \"21K (Omicron)\", \"#DB2823\" ],"
+      "        [ \"21L (Omicron)\", \"#DB2823\" ],"
+      "        [ \"21M (Omicron)\", \"#DB2823\" ],"
       "        [ \"uploaded sample\", \"#FF0000\" ] ],"
       "    \"title\": \"Nextstrain Clade\", \"type\": \"categorical\" },"
       , outF);
 if (sameString(source, "GISAID"))
     fputs("  { \"key\": \"GISAID_clade\","
       "    \"scale\": [ [ \"S\", \"#EC676D\" ], [ \"L\", \"#F79E43\" ], [ \"O\", \"#F9D136\" ],"
       "        [ \"V\", \"#FAEA95\" ], [ \"G\", \"#B6D77A\" ], [ \"GH\", \"#8FD4ED\" ],"
       "        [ \"GR\", \"#A692C3\" ] ],"
       "    \"title\": \"GISAID Clade\", \"type\": \"categorical\" },"
           , outF);
 fprintf(outF,
       "  { \"key\": \"pango_lineage_usher\", "
       "    \"title\": \"Pango lineage assigned by UShER\", \"type\": \"categorical\" },"
       "  { \"key\": \"Nextstrain_clade_usher\","
       "    \"scale\": [ "
-      "        [ \"20H(Beta, V2)\", \"#3F47C9\" ],"
-      "        [ \"20I(Alpha, V1)\", \"#4274CE\" ],"
-      "        [ \"20J(Gamma, V3)\", \"#4F97BB\" ],"
-      "        [ \"21A(Delta)\", \"#64AC99\" ],"
-      "        [ \"21B(Kappa)\", \"#7EB976\" ],"
-      "        [ \"21C(Epsilon)\", \"#9EBE5A\" ],"
-      "        [ \"21D(Eta)\", \"#BEBB48\" ],"
-      "        [ \"21E(Theta)\", \"#D9AE3E\" ],"
-      "        [ \"21F(Iota)\", \"#E69036\" ],"
-      "        [ \"21G(Lambda)\", \"#E35F2D\" ],"
-      "        [ \"20H (Beta, V2)\", \"#3F47C9\" ],"
-      "        [ \"20I (Alpha, V1)\", \"#4274CE\" ],"
-      "        [ \"20J (Gamma, V3)\", \"#4F97BB\" ],"
-      "        [ \"21A (Delta)\", \"#64AC99\" ],"
-      "        [ \"21B (Kappa)\", \"#7EB976\" ],"
-      "        [ \"21C (Epsilon)\", \"#9EBE5A\" ],"
-      "        [ \"21D (Eta)\", \"#BEBB48\" ],"
-      "        [ \"21E (Theta)\", \"#D9AE3E\" ],"
-      "        [ \"21F (Iota)\", \"#E69036\" ],"
-      "        [ \"21G (Lambda)\", \"#E35F2D\" ],"
-      "        [ \"21H\", \"#DB2823\" ],"
+      "        [ \"20H (Beta, V2)\", \"#571EA2\" ],"
+      "        [ \"20I (Alpha, V1)\", \"#4334BF\" ],"
+      "        [ \"20J (Gamma, V3)\", \"#3F55CE\" ],"
+      "        [ \"20H (Beta,V2)\", \"#571EA2\" ],"
+      "        [ \"20I (Alpha,V1)\", \"#4334BF\" ],"
+      "        [ \"20J (Gamma,V3)\", \"#3F55CE\" ],"
+      "        [ \"21A (Delta)\", \"#4376CD\" ],"
+      "        [ \"21I (Delta)\", \"#4C91C0\" ],"
+      "        [ \"21J (Delta)\", \"#59A4A9\" ],"
+      "        [ \"21C (Epsilon)\", \"#7FB975\" ],"
+      "        [ \"21D (Eta)\", \"#97BD5F\" ],"
+      "        [ \"21F (Iota)\", \"#C7B944\" ],"
+      "        [ \"21G (Lambda)\", \"#D9AD3D\" ],"
+      "        [ \"21H (Mu)\", \"#E49838\" ],"
+      "        [ \"21K (Omicron)\", \"#DB2823\" ],"
+      "        [ \"21L\", \"#DB2823\" ],"
+      "        [ \"21L (Omicron)\", \"#DB2823\" ],"
+      "        [ \"21M (Omicron)\", \"#DB2823\" ],"
       "        [ \"uploaded sample\", \"#FF0000\" ] ],"
       "    \"title\": \"Nextstrain Clade assigned by UShER\", \"type\": \"categorical\" },"
         "  { \"key\": \"userOrOld\", "
         "    \"scale\": [ [ \"uploaded sample\", \"#CC0000\"] , [ \"%s\", \"#000000\"] ],"
         "    \"title\": \"Sample type\", \"type\": \"categorical\" },"
         "  {\"key\": \"gt\", \"title\": \"Genotype\", \"type\": \"categorical\"},"
         "  {\"key\": \"country\", \"title\": \"Country\", \"type\": \"categorical\"}"
         , source);
 fputs("  ] , "
 //#*** Filters didn't seem to work... maybe something about the new fetch feature, or do I need to spcify in some other way?
 //#***      "\"filters\": [ \"GISAID_clade\", \"region\", \"country\", \"division\", \"author\" ], "
       "\"filters\": [ ], "
       "\"genome_annotations\":"
       "{\"E\":{\"end\":26472,\"start\":26245,\"strand\":\"+\",\"type\":\"CDS\"},"
       " \"M\":{\"end\":27191,\"start\":26523,\"strand\":\"+\",\"type\":\"CDS\"},"