bb1f29a4c6d5222beb5d51c05486fefaa763da51
jnavarr5
  Wed Apr 15 13:27:07 2026 -0700
Printing out how to force the update if the itemCheck fails for genCC, no Redmine

diff --git src/hg/utils/otto/genCC/doGenCC.py src/hg/utils/otto/genCC/doGenCC.py
index 9c10b3e173a..501a6c28cec 100644
--- src/hg/utils/otto/genCC/doGenCC.py
+++ src/hg/utils/otto/genCC/doGenCC.py
@@ -295,35 +295,36 @@
         return(True)
     elif args.force:
         # Previous file matches current file, but update didn't go through
         # because of itemCounts check.
         return(True)
     else:
         return(False)
 
 def checkItemCounts(oldBb, newBb):
     """Compare item counts between old and new bigBed files. Exit if difference > 10%."""
     oldItemCount = bash('bigBedInfo '+oldBb+' | grep "itemCount"')
     oldItemCount = int(oldItemCount.rstrip().split("itemCount: ")[1].replace(",",""))
     newItemCount = bash('bigBedInfo '+newBb+' | grep "itemCount"')
     newItemCount = int(newItemCount.rstrip().split("itemCount: ")[1].replace(",",""))
     if abs(newItemCount - oldItemCount) > 0.1 * max(newItemCount, oldItemCount):
-        msg = "Item count difference >10% for "+newBb+":\nold="+str(oldItemCount)+" new="+str(newItemCount)
+        msg = "WARNING:\nItem count difference >10% for "+newBb+":\nold="+str(oldItemCount)+" new="+str(newItemCount)
+        print(msg)
         if args.force:
-            print("WARNING:\n"+msg+"\n(continuing due to QA approval)")
+            print("(continuing due to QA approval)")
         else:
-            sys.exit(msg)
+            sys.exit("Run ./doGenCC.py --force if you approve the item count change.")
     print(oldBb+" old: "+str(oldItemCount)+" new: "+str(newItemCount))
 
 if checkIfUpdateIsNeeded():
     date = str(datetime.now()).split(" ")[0]
     workDir = "/hive/data/outside/otto/genCC/"+date
     bash("mkdir -p "+workDir)
     hg19outPutFile = workDir+"/hg19genCC.bed"
     hg38outPutFile = workDir+"/hg38genCC.bed"
     bash("cp /hive/data/outside/otto/genCC/newSubmission.tsv "+workDir)
     genCCtsvFile = "/hive/data/outside/otto/genCC/newSubmission.tsv"
 
     # Auto-detect latest GENCODE Comprehensive tables
     gencodeHg38 = getLatestGencodeTable('hg38', 'wgEncodeGencodeComp%')
     gencodeHg19 = getLatestGencodeTable('hg19', 'wgEncodeGencodeComp%lift37')