0a01cd0845e94f390d6522016c6caf247ba36b96
angie
  Thu Jul 1 17:25:59 2021 -0700
Adding Auspice colorings contributed by @babarlelephant in github PR #57.

diff --git src/hg/hgPhyloPlace/treeToAuspiceJson.c src/hg/hgPhyloPlace/treeToAuspiceJson.c
index b7987b3..e94b5c3 100644
--- src/hg/hgPhyloPlace/treeToAuspiceJson.c
+++ src/hg/hgPhyloPlace/treeToAuspiceJson.c
@@ -44,36 +44,52 @@
       "        [ \"20E (EU1)\", \"#44CC44\" ], [ \"20F\", \"#8822AA\" ],"
       "        [ \"20G\", \"#8888FF\" ], [ \"20H/501Y.V2\", \"#6666FF\" ],"
       "        [ \"20I/501Y.V1\", \"#CC44EE\" ], [ \"20A.EU2\", \"#448844\"  ], "
       "        [ \"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\": \"userOrOld\", "
         "    \"scale\": [ [ \"uploaded sample\", \"#CC0000\"] , [ \"%s\", \"#000000\"] ],"
-        "    \"title\": \"Sample type\", \"type\": \"categorical\" }"
+        "    \"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\"},"
+      " \"N\":{\"end\":29533,\"start\":28274,\"strand\":\"+\",\"type\":\"CDS\"},"
+      " \"ORF1a\":{\"end\":13468,\"start\":266,\"strand\":\"+\",\"type\":\"CDS\"},"
+      " \"ORF1b\":{\"end\":21555,\"start\":13468,\"strand\":\"+\",\"type\":\"CDS\"},"
+      " \"ORF3a\":{\"end\":26220,\"start\":25393,\"strand\":\"+\",\"type\":\"CDS\"},"
+      " \"ORF6\":{\"end\":27387,\"start\":27202,\"strand\":\"+\",\"type\":\"CDS\"},"
+      " \"ORF7a\":{\"end\":27759,\"start\":27394,\"strand\":\"+\",\"type\":\"CDS\"},"
+      " \"ORF7b\":{\"end\":27887,\"start\":27756,\"strand\":\"+\",\"type\":\"CDS\"},"
+      " \"ORF8\":{\"end\":28259,\"start\":27894,\"strand\":\"+\",\"type\":\"CDS\"},"
+      " \"ORF9b\":{\"end\":28577,\"start\":28284,\"strand\":\"+\",\"type\":\"CDS\"},"
+      " \"S\":{\"end\":25384,\"start\":21563,\"strand\":\"+\",\"type\":\"CDS\"},"
+      " \"nuc\":{\"end\":29903,\"start\":1,\"strand\":\"+\",\"type\":\"source\"}},"
       "\"display_defaults\": { "
       "  \"branch_label\": \"none\", "
       "  \"color_by\": \"Nextstrain_clade\" "
       "}, "
       , outF);
 fprintf(outF,
         "\"description\": \"Dataset generated by [UShER web interface]"
         "(%shgPhyloPlace) using the "
         "[usher](https://github.com/yatisht/usher/) program.  "
 //#*** TODO: describe input from which tree was generated: user sample, version of tree, etc.
         , hLocalHostCgiBinUrl());
 fputs("If you have metadata you wish to display, you can now drag on a CSV file and it will be "
       "added into this view, [see here]("NEXTSTRAIN_DRAG_DROP_DOC") "
       "for more info.\"} ,"
       , outF);