b82dc4064ed8467e65e54bf87ca1888b075d579a
max
  Wed Jun 8 01:38:47 2022 -0700
small fix to clinvar otto job, no redmine

diff --git src/hg/utils/otto/clinvar/clinVarToBed src/hg/utils/otto/clinvar/clinVarToBed
index 8b3e581..a624c3d 100755
--- src/hg/utils/otto/clinvar/clinVarToBed
+++ src/hg/utils/otto/clinvar/clinVarToBed
@@ -735,30 +735,35 @@
     else:
         print("Invalid assembly: %s, row %s" % (repr(assembly), repr(row)))
         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 chrom=="Un":
+        print("Unknown fix/alt/patch chrom, please adapt clinVarToBed")
+        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)