34277489b7571b02a541eb567ab88f3383c56ecb
jnavarr5
  Tue Jul 29 12:29:33 2025 -0700
Fixing a typo in the pipefail line, no Redmine

diff --git src/hg/utils/otto/varChat/varChatOtto.sh src/hg/utils/otto/varChat/varChatOtto.sh
index 7186990dbce..b8b3092825b 100755
--- src/hg/utils/otto/varChat/varChatOtto.sh
+++ src/hg/utils/otto/varChat/varChatOtto.sh
@@ -1,54 +1,54 @@
 #!/bin/bash
 
-set -e -o pipefile
+set -e -o pipefail
 
 cd /hive/data/outside/otto/varChat
 
 wget -q https://ucsc-engenome-varchat.s3.eu-west-1.amazonaws.com/latest/VarChat_GRCh38_latest.bb -O varChat.hg38.latest.bb
 wget -q https://ucsc-engenome-varchat.s3.eu-west-1.amazonaws.com/latest/VarChat_GRCh37_latest.bb -O varChat.hg19.latest.bb
 
 # Check if the files are the same
 if cmp -s varChat.hg38.latest.bb varChat.hg38.bb; then
   # Files are the same, exit silently
   rm varChat.hg38.latest.bb
   rm varChat.hg19.latest.bb
   exit 0
 else
   # Files are different, continue with the script or add actions
   echo "Updating VarChat track..."
 fi
 
 oldCountHg38=$(bigBedInfo varChat.hg38.bb | grep -i "itemCount" | awk '{print $NF}')
 oldCountHg19=$(bigBedInfo varChat.hg19.bb | grep -i "itemCount" | awk '{print $NF}')
 
 newCountHg38=$(bigBedInfo varChat.hg38.latest.bb | grep -i "itemCount" | awk '{print $NF}')
 newCountHg19=$(bigBedInfo varChat.hg19.latest.bb | grep -i "itemCount" | awk '{print $NF}')
 
 # Calculate the percentage difference
 diffHg38=$(echo "scale=2; (($newCountHg38 - $oldCountHg38) / $oldCountHg38) * 100" | bc)
 diffHg19=$(echo "scale=2; (($newCountHg19 - $oldCountHg19) / $oldCountHg19) * 100" | bc)
 
 # Get the absolute values of the differences
 absDiffHg38=$(echo "$diffHg38" | sed 's/-//')
 absDiffHg19=$(echo "$diffHg19" | sed 's/-//')
 
 # Check if the absolute difference is greater than 20%
 if (( $(echo "$absDiffHg38 > 20" | bc -l) || $(echo "$absDiffHg19 > 20" | bc -l) )); then
     echo
     echo "Error: Difference in item count exceeds 20%."
     echo "Difference in hg38: $diffHg38%"
     echo "Difference in hg19: $diffHg19%"
     exit 1
 fi
 
 # If the difference is within the 20%, proceed
 mv varChat.hg38.latest.bb varChat.hg38.bb
 mv varChat.hg19.latest.bb varChat.hg19.bb
 
 wget -q https://ucsc-engenome-varchat.s3.eu-west-1.amazonaws.com/latest/version.txt -O version.txt
 
 echo
 echo "Item counts for hg38 old vs. new bigBed. Old: $oldCountHg38 New: $newCountHg38"
 echo "Item counts for hg19 old vs. new bigBed. Old: $oldCountHg19 New: $newCountHg19"
 echo
 echo "VarChat track built successfully."