d642cf5039fe119b031d57590a4d9644bf9d90fa
max
  Mon Dec 16 05:49:18 2024 -0800
bed9 fix for revel overlap track, due to my oversight in previous commit, refs #34947

diff --git src/hg/makeDb/revel/revelToWig.py src/hg/makeDb/revel/revelToWig.py
index 6dffeae..52cc779 100644
--- src/hg/makeDb/revel/revelToWig.py
+++ src/hg/makeDb/revel/revelToWig.py
@@ -40,31 +40,31 @@
     for alt, scoreTransList in prevTransIds.items():
         tableDict = {}
         tableLines = []
         mouseOvers = []
         allScores = set()
         for revelScore, transIdStr in scoreTransList:
             mouseOvers.append("transcript %s -> score %f" % (transIdStr, revelScore))
             #tableLines.append(transIdStr.replace(",", ", ")+"|"+str(revelScore))
             assert(transIdStr not in tableDict)
             tableDict[transIdStr] = str(revelScore)
             allScores.add(revelScore)
 
         # ONLY output the line if we have different scores = there is no need to output a feature if all the scores are the same
         if len(allScores)>1:
             #bed = (chrom, start, start+1, ref+">"+alt, "0", ".", start, start+1, ";".join(tableLines), ", ".join(mouseOvers))
-            bed = (chrom, start, start+1, ref+">"+alt, "0", ".", start, start+1, json.dumps(tableDict), ", ".join(mouseOvers))
+            bed = (chrom, start, start+1, ref+">"+alt, "0", ".", start, start+1, "0,0,0", json.dumps(tableDict), ", ".join(mouseOvers))
             bed = [str(x) for x in bed]
             bedFh.write("\t".join(bed))
             bedFh.write("\n")
 
 def inputLineChunk(fname, chromSizes, db):
     " read all values for one chrom and return as four arrays, -1 means 'no value'"
     # chr,hg19_pos,grch38_pos,ref,alt,aaref,aaalt,REVEL
     values = []
     prevTransIds = defaultdict(list)
 
     if fname.endswith(".gz"):
         ifh = subprocess.Popen(['zcat', fname], stdout=subprocess.PIPE, encoding="ascii").stdout
     else:
         ifh = open(fname)