c0a8cbabcde0c34dd630b98c16c603d8ff8feb90
max
  Mon Aug 14 08:53:39 2023 -0700
adding VCV id to clinvar hgc page, refs #31966

diff --git src/hg/utils/otto/clinvar/clinVarToBed src/hg/utils/otto/clinvar/clinVarToBed
index 7fe96d2..85c298c 100755
--- src/hg/utils/otto/clinvar/clinVarToBed
+++ src/hg/utils/otto/clinvar/clinVarToBed
@@ -737,32 +737,37 @@
         assert(False)
 
     #hgvsTable =  ";".join(hgvs[alleleId])
     hgvsTable =  json.dumps(hgvs[alleleId])
 
     molConseq = allToVcf.get(int(alleleId))
     if molConseq is None:
         logging.debug("%s has no molConseq" % alleleId)
         noMcCount += 1
         molConseq = ""
 
     if chromAcc=="NT_187513.1":
         chrom = "chrUn_KI270742v1"
     elif chromAcc=="NT_167222.1":
         chrom = "chrUn_gl000228"
+    elif chromAcc=="NT_113889.1":
+        if assembly=="GRCh37":
+            chrom = "chrUn_gl000218"
+        else:
+            chrom = "chrUn_GL000218v1"
     elif chrom=="Un":
-        print("Unknown fix/alt/patch chrom, please adapt clinVarToBed")
+        print("Unknown fix/alt/patch chrom, please adapt clinVarToBed: %s, row: %s" % (chrom, row))
         sys.exit(1)
     else:
         chrom = "chr"+chrom
 
     if chrom=="chrUn" and assembly=="GRCh38":
         print(("wrong chrUn chrom on assembly hg38. Skipping %s" % irvcAcc))
         continue
 
     if chrom=="chrMT": # why does NCBI use chrMT but we use chrM ?
         if assembly=="GRCh37":
             chrom = "chrMT" # our chrM is different from NCBI's MT, but chrMT got added hg19 in 2020 
         else:
             chrom = "chrM"
 
     shortName, longName = shortenName(name)
@@ -851,31 +856,33 @@
         geneStr = "not shown, too many genes"
 
     mouseOverName = name
 
     otherIds, dbVarSsvAcc = accListToHtml(otherIds)
 
     if isCnv and dbVarSsvAcc!="":
         shortName = dbVarSsvAcc
     elif name=="":
         name = "No display name was provided by ClinVar for this variant"
         shortName = "NoName"
         mouseOverName = ""
 
     if len(name)>90:
         name = name[:90]+"..."
-    name = varId+"|"+name
+
+    vcvId = "VCV%09d" % int(varId)
+    name = varId+"|"+vcvId+" : "+name
 
     if len(mouseOverName)>80:
         mouseOverName = mouseOverName[:80]+"..."
 
     #if len(hgvsProt) > 90:
         #hgvsProt = hgvsProt[:90]+"..."
     #if len(hgvsCod) > 90:
         #hgvsCod = hgvsCod[:90]+"..."
 
     phenotypeIds, _ = accListToHtml(phenotypeIds)
 
     starRatingHtml, asciiStars, starCount = reviewStatusToHtmlStars(reviewStatus)
 
     phenotypeList = ", ".join(phenotypeList.split("|"))