761e0687825ec835c5a8598d537ac1f311263c79
angie
  Mon Dec 5 16:18:56 2011 -0800
Feature #6172 (ISCA track tweaks): per ISCA's requests, change"Structural variant cluster" to "Variant region", add link to dbVar's
variant page, and add link to dbVar's page for the ISCA study (nstd37).

diff --git src/hg/hgc/gvfClick.c src/hg/hgc/gvfClick.c
index 4c042aa..7593575 100644
--- src/hg/hgc/gvfClick.c
+++ src/hg/hgc/gvfClick.c
@@ -20,31 +20,31 @@
 void doGvf(struct trackDb *tdb, char *item)
 /* Show details for variants represented as GVF, stored in a bed8Attrs table */
 {
 struct sqlConnection *conn = hAllocConn(database);
 int start = cartInt(cart, "o");
 char query[1024];
 safef(query, sizeof(query),
       "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d",
       tdb->table, item, seqName, start);
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row;
 if ((row = sqlNextRow(sr)) == NULL)
     errAbort("doGvfDetails: can't find item '%s' in %s at %s:%d", item, database, seqName, start);
 int rowOffset = hOffsetPastBin(database, seqName, tdb->table);
 struct bed8Attrs *ba = bed8AttrsLoad(row+rowOffset);
-bedPrintPos((struct bed *)ba, 6, tdb);
+bedPrintPos((struct bed *)ba, 3, tdb);
 int i = 0;
 // Note: this loop modifies ba->attrVals[i], assuming we won't use them again:
 for (i = 0;  i < ba->attrCount;  i++)
     {
     // The ID is the bed8Attrs name and has already been displayed:
     if (sameString(ba->attrTags[i], "ID"))
 	continue;
     cgiDecode(ba->attrVals[i], ba->attrVals[i], strlen(ba->attrVals[i]));
     char *tag = ba->attrTags[i];
     // User-defined keywords used in dbVar's GVF:
     if (sameString(tag, "var_type")) // This one isn't anymore, but I add it back (hg18.txt).
 	tag = "Variant type";
     else if (sameString(tag, "clinical_int"))
 	tag = "Clinical interpretation";
     else if (sameString(tag, "var_origin"))
@@ -71,27 +71,29 @@
 		rangeEnd = "unknown";
 	    if (isStartRange)
 		printf("<B>Start range</B>: outer start %s, inner start %s<BR>\n",
 		       rangeStart, rangeEnd);
 	    else
 		printf("<B>End range</B>: inner end %s, outer end %s<BR>\n",
 		       rangeStart, rangeEnd);
 	    }
 	else
 	    // not formatted as expected, just print as-is:
 	    printf("<B>%s</B>: %s<BR>\n", tag, htmlEncode(ba->attrVals[i]));
 	}
     // Parent sounds like mom or dad (as in var_origin)... tweak it too:
     else if (sameString(tag, "Parent"))
 	{
-	printf("<B>Structural variant cluster:</B> %s<BR>\n", htmlEncode(ba->attrVals[i]));
+	printf("<B>Variant region:</B> "
+	       "<A HREF=\"http://www.ncbi.nlm.nih.gov/dbvar/variants/%s/\" "
+	       "TARGET=_BLANK>%s</A><BR>\n", ba->attrVals[i], htmlEncode(ba->attrVals[i]));
 	}
     else
 	{
 	subChar(tag, '_', ' ');
 	printf("<B>%s</B>: %s<BR>\n", tag, htmlEncode(ba->attrVals[i]));
 	}
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 /* printTrackHtml is done in genericClickHandlerPlus. */
 }