742602cf67e7fa9cb6584bbefe1512774b8277bc
jnavarr5
  Wed Dec 17 15:25:41 2025 -0800
Sorting the input file for the bedToBigBed command, no Redmine.

diff --git src/hg/utils/otto/genCC/doGenCC.py src/hg/utils/otto/genCC/doGenCC.py
index e821f5efb02..a898b31c08f 100644
--- src/hg/utils/otto/genCC/doGenCC.py
+++ src/hg/utils/otto/genCC/doGenCC.py
@@ -228,29 +228,29 @@
     
 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"
          
     buildFileHg38(genCCtsvFile,hg38outPutFile)
     buildFileHg19(hg38outPutFile,hg19outPutFile)
     bash("mv /hive/data/outside/otto/genCC/newSubmission.tsv /hive/data/outside/otto/genCC/prevSubmission.tsv")
 
     bash("bedSort "+hg38outPutFile+" "+hg38outPutFile)
-    bash("bedToBigBed -as=/hive/data/genomes/hg38/bed/genCC/genCC.as -extraIndex=gene_symbol -type=bed9+33 -tab "+hg38outPutFile+" /cluster/data/hg38/chrom.sizes "+hg38outPutFile.split(".")[0]+".bb")
+    bash("bedToBigBed -as=/hive/data/genomes/hg38/bed/genCC/genCC.as -sort -extraIndex=gene_symbol -type=bed9+33 -tab "+hg38outPutFile+" /cluster/data/hg38/chrom.sizes "+hg38outPutFile.split(".")[0]+".bb")
     print("Final file created: "+hg38outPutFile.split(".")[0]+".bb")
 
     bash("bedSort "+hg19outPutFile+" "+hg19outPutFile)
-    bash("bedToBigBed -as=/hive/data/genomes/hg38/bed/genCC/genCC.as -extraIndex=gene_symbol -type=bed9+33 -tab "+hg19outPutFile+" /cluster/data/hg19/chrom.sizes "+hg19outPutFile.split(".")[0]+".bb")
+    bash("bedToBigBed -as=/hive/data/genomes/hg38/bed/genCC/genCC.as -sort -extraIndex=gene_symbol -type=bed9+33 -tab "+hg19outPutFile+" /cluster/data/hg19/chrom.sizes "+hg19outPutFile.split(".")[0]+".bb")
     print("Final file created: "+hg19outPutFile.split(".")[0]+".bb")
          
     bash("rm -f /gbdb/hg38/bbi/genCC.bb")
     bash("rm -f /gbdb/hg19/bbi/genCC.bb")
          
     bash("ln -s "+hg38outPutFile.split(".")[0]+".bb /gbdb/hg38/bbi/genCC.bb")
     bash("ln -s "+hg19outPutFile.split(".")[0]+".bb /gbdb/hg19/bbi/genCC.bb")
          
     print("GenCC updated.")