71c6d9c65dcbb95c4c1840a2409e7457aed62c66
markd
  Wed Jul 17 19:21:15 2019 -0700
removed links to HAVANA as database is archives and HAVANA ids are on their way out

diff --git src/hg/hgc/gencodeClick.c src/hg/hgc/gencodeClick.c
index 95561c0..953ccc9 100644
--- src/hg/hgc/gencodeClick.c
+++ src/hg/hgc/gencodeClick.c
@@ -37,33 +37,30 @@
 
 /* Various URLs and URL templates.  At one time, these were in the ra file,
  * but that didn't prove that helpful and end up requiring updated the ra
  * files for every GENCODE version if a URL was added or changed. */
 //FIXME: clean up RA files when CGIs no longer need them
 static char *ensemblTranscriptIdUrl = "http://www.ensembl.org/%s/Transcript/Summary?db=core;t=%s";
 static char *ensemblGeneIdUrl = "http://www.ensembl.org/%s/Gene/Summary?db=core;t=%s";
 static char *ensemblProteinIdUrl = "http://www.ensembl.org/%s/Transcript/ProteinSummary?db=core;t=%s";
 static char *ensemblSupportingEvidUrl = "http://www.ensembl.org/%s/Transcript/SupportingEvidence?db=core;t=%s";
 
 static char *ensemblH37TranscriptIdUrl = "http://grch37.ensembl.org/%s/Transcript/Summary?db=core;t=%s";
 static char *ensemblH37GeneIdUrl = "http://grch37.ensembl.org/%s/Gene/Summary?db=core;t=%s";
 static char *ensemblH37ProteinIdUrl = "http://grch37.ensembl.org/%s/Transcript/ProteinSummary?db=core;t=%s";
 static char *ensemblH37SupportingEvidUrl = "http://grch37.ensembl.org/%s/Transcript/SupportingEvidence?db=core;t=%s";
 
-static char *vegaTranscriptIdUrl = "http://vega.sanger.ac.uk/%s/Transcript/Summary?db=core;t=%s";
-static char *vegaGeneIdUrl = "http://vega.sanger.ac.uk/%s/Gene/Summary?db=core;g=%s";
-
 static char *gencodeBiotypesUrl = "http://www.gencodegenes.org/pages/biotypes.html";
 static char *gencodeTagsUrl = "http://www.gencodegenes.org/pages/tags.html";
 
 static char *yalePseudoUrl = "http://tables.pseudogene.org/%s";
 static char *hgncUrl = " https://www.genenames.org/data/gene-symbol-report/#!/symbol/%s";
 static char *geneCardsUrl = "http://www.genecards.org/cgi-bin/carddisp.pl?gene=%s";
 static char *apprisHomeUrl = "http://appris-tools.org/";
 static char *apprisGeneUrl = "http://appris-tools.org/#/database/id/%s/%s?sc=ensembl";
 
 static char *getBaseAcc(char *acc, char *accBuf, int accBufSize)
 /* get the accession with version number dropped. */
 {
 safecpy(accBuf, accBufSize, acc);
 char *dot = strchr(accBuf, '.');
 if (dot != NULL)
@@ -255,48 +252,48 @@
     safef(urlBuf, sizeof(urlBuf), urlTemplate, id);
     printf("<a href=\"%s\" target=_blank>%s</a>", urlBuf, id);
     }
 }
 
 #if UNUSED
 static void prTdExtIdAnchor(char *id, char *urlTemplate)
 /* print a table data element with an anchor for a id */
 {
 printf("<td>");
 prExtIdAnchor(id, urlTemplate);
 }
 #endif
 
 static void prEnsIdAnchor(char *id, char *urlTemplate)
-/* if an id to an ensembl or vega database is not empty, print an HTML anchor to it */
+/* if an id to an ensembl database is not empty, print an HTML anchor to it */
 {
 if (!isEmpty(id))
     {
     char idBuf[64], urlBuf[512];
     /* The lift37 releases append a '_N' modifier to the ids to indicate the are
      * mapped. N is an integer mapping version. Don't include this in link if it exists. */
     safecpy(idBuf, sizeof(idBuf), id);
     char *p = strchr(idBuf, '_');
     if (p != NULL)
         *p = '\0';
     safef(urlBuf, sizeof(urlBuf), urlTemplate, getScientificNameSym(), idBuf);
     printf("<a href=\"%s\" target=_blank>%s</a>", urlBuf, id);
     }
 }
 
 static void prTdEnsIdAnchor(char *id, char *urlTemplate)
-/* print a table data element with an ensembl/vega anchor for a id */
+/* print a table data element with an ensembl anchor for a id */
 {
 printf("<td>");
 prEnsIdAnchor(id, urlTemplate);
 }
 
 static void prApprisTdAnchor(char *id, char *label, char *urlTemplate)
 /* print a gene or transcript link to APPRIS */
 {
 // under bar separated, lower case species name.
 char *speciesArg = hScientificName(database);
 toLowerN(speciesArg, strlen(speciesArg));
 subChar(speciesArg, ' ', '_');
 
 char accBuf[64];
 printf("<td><a href=\"");
@@ -396,32 +393,32 @@
 
 if (transAttrs->proteinId != NULL)
     {
     // protein id in database, maybe not for this transcript
     printf("<tr><th>Protein id");
     if (strlen(transAttrs->proteinId) > 0)
         prTdEnsIdAnchor(transAttrs->proteinId,
                         (isGrcH37Native(tdb) ? ensemblH37ProteinIdUrl: ensemblProteinIdUrl));
     else
         printf("<td>&nbsp;");
     printf("<td>");
     printf("</tr>\n");
     }
 
 printf("<tr><th>HAVANA manual id");
-prTdEnsIdAnchor(transAttrs->havanaTranscriptId, vegaTranscriptIdUrl);
-prTdEnsIdAnchor(transAttrs->havanaGeneId, vegaGeneIdUrl);
+printf("<td>%s", transAttrs->havanaTranscriptId);
+printf("<td>%s", transAttrs->havanaGeneId);
 printf("</tr>\n");
 
 printf("<tr><th>Position");
 printf("<td>");
 writePosLink(transAnno->chrom, transAnno->txStart, transAnno->txEnd);
 printf("<td>");
 writePosLink(transAnno->chrom, geneChromStart, geneChromEnd);
 printf("</tr>\n");
 
 printf("<tr><th>Strand<td>%s<td></tr>\n", transAnno->strand);
 
 printf("<tr><th><a href=\"%s\" target = _blank>Biotype</a><td>%s<td>%s</tr>\n", gencodeBiotypesUrl, transAttrs->transcriptType, transAttrs->geneType);
 
 printf("<tr><th>Annotation Level<td>%s (%d)<td></tr>\n", getLevelDesc(transAttrs->level), transAttrs->level);