9364a4054ae5065f07014618eef211a85a4b8c1f
jnavarr5
  Wed Apr 15 13:07:01 2026 -0700
Have --force bypass the md5sum update check in genCC otto, no redmine.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

diff --git src/hg/utils/otto/genCC/doGenCC.py src/hg/utils/otto/genCC/doGenCC.py
index 3059a5b8ad6..170f1316cc4 100644
--- src/hg/utils/otto/genCC/doGenCC.py
+++ src/hg/utils/otto/genCC/doGenCC.py
@@ -281,30 +281,34 @@
             outputHg19File.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (chrom,chromStart,chromEnd,
                                     "\t".join(line[3:6]),chromStart,chromEnd,"\t".join(line[8:])))
 
     print("hg19 genCC bed file completed. Total number of failed entries: "+str(n))
     if skippedCoords > 0:
         print("Warning: "+str(skippedCoords)+" hg19 entries skipped due to inverted coordinates")
 
 def checkIfUpdateIsNeeded():
     bash("wget -q 'https://thegencc.org/download/action/submissions-export-tsv?format=new' -O /hive/data/outside/otto/genCC/newSubmission.tsv")
     newMd5sum = bash("md5sum /hive/data/outside/otto/genCC/newSubmission.tsv")
     newMd5sum = newMd5sum.split("  ")[0]
     oldMd5sum = bash("md5sum /hive/data/outside/otto/genCC/prevSubmission.tsv")
     oldMd5sum = oldMd5sum.split("  ")[0]
     if oldMd5sum != newMd5sum:
         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+": old="+str(oldItemCount)+" new="+str(newItemCount)
         if args.force:
             print("WARNING:\n "+msg+"\n\n (continuing due to QA approval)")
         else:
             sys.exit(msg)