3bff5347fbcb13f51d78425f0c53009cd466f8b8
angie
  Fri Oct 15 09:46:33 2021 -0700
Auspice JSON: define ORF1ab not ORF1a/ORF1b as suggested by Cornelius Roemer in https://github.com/yatisht/usher/issues/174

diff --git src/hg/hgPhyloPlace/treeToAuspiceJson.c src/hg/hgPhyloPlace/treeToAuspiceJson.c
index 978e603..9297fa9 100644
--- src/hg/hgPhyloPlace/treeToAuspiceJson.c
+++ src/hg/hgPhyloPlace/treeToAuspiceJson.c
@@ -90,32 +90,33 @@
       "    \"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\"},"
       " \"N\":{\"end\":29533,\"start\":28274,\"strand\":\"+\",\"type\":\"CDS\"},"
-      " \"ORF1a\":{\"end\":13468,\"start\":266,\"strand\":\"+\",\"type\":\"CDS\"},"
-      " \"ORF1b\":{\"end\":21555,\"start\":13468,\"strand\":\"+\",\"type\":\"CDS\"},"
+      " \"ORF1ab\":{\"end\":21555,\"start\":266,\"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]"