36f39e904ea59703ae48ff8a690cf25675dd6af1
angie
  Mon Aug 1 09:47:06 2011 -0700
Feature #2823 (VCF track handler): in hgc, let the user know when wecan't access the file (instead of just displaying nothing) and include
custom url.

diff --git src/hg/hgc/vcfClick.c src/hg/hgc/vcfClick.c
index 4339481..00fa4b0 100644
--- src/hg/hgc/vcfClick.c
+++ src/hg/hgc/vcfClick.c
@@ -216,30 +216,31 @@
 if (hTableExists(database, "knownGene"))
     {
     struct pgSnp *pgs = pgSnpFromVcfRecord(rec);
     if (!sameString(rec->chrom, seqName))
 	// rec->chrom might be missing "chr" prefix:
 	pgs->chrom = seqName;
     printSeqCodDisplay(database, pgs);
     }
 }
 
 static void vcfRecordDetails(struct trackDb *tdb, struct vcfRecord *rec)
 /* Display the contents of a single line of VCF, assumed to be from seqName
  * (using seqName instead of rec->chrom because rec->chrom might lack "chr"). */
 {
 printf("<B>Name:</B> %s<BR>\n", rec->name);
+printCustomUrl(tdb, rec->name, TRUE);
 static char *formName = "vcfCfgHapCenter";
 printf("<FORM NAME=\"%s\" ACTION=\"%s\">\n", formName, hgTracksName());
 vcfCfgHaplotypeCenter(cart, tdb, rec->file, rec->name, seqName, rec->chromStart, formName);
 printf("</FORM>\n");
 printPosOnChrom(seqName, rec->chromStart, rec->chromEnd, NULL, FALSE, rec->name);
 printf("<B>Reference allele:</B> %s<BR>\n", rec->ref);
 vcfAltAlleleDetails(rec);
 vcfQualDetails(rec);
 vcfFilterDetails(rec);
 vcfInfoDetails(rec);
 pgSnpCodingDetail(rec);
 // Wrapper table for collapsible section:
 puts("<TABLE>");
 vcfGenotypesDetails(rec, tdb->track);
 puts("</TABLE>");
@@ -269,19 +270,21 @@
     }
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     {
     if (isNotEmpty(errCatch->message->string))
 	warn("%s", errCatch->message->string);
     }
 errCatchFree(&errCatch);
 if (vcff != NULL)
     {
     struct vcfRecord *rec;
     for (rec = vcff->records;  rec != NULL;  rec = rec->next)
 	if (rec->chromStart == start && rec->chromEnd == end) // in pgSnp mode, don't get name
 	    vcfRecordDetails(tdb, rec);
     }
+else
+    printf("Sorry, unable to open %s<BR>\n", fileOrUrl);
 }
 
 
 #endif // no USE_TABIX