5253452667b95976d5b2f10a20d2b509306f4406
lrnassar
  Fri Feb 7 13:45:49 2025 -0800
Adding VarChat track to otto, refs #35197

diff --git src/hg/utils/otto/varChat/varChatOtto.sh src/hg/utils/otto/varChat/varChatOtto.sh
new file mode 100755
index 00000000000..6e52890791f
--- /dev/null
+++ src/hg/utils/otto/varChat/varChatOtto.sh
@@ -0,0 +1,52 @@
+#! /bin/bash
+
+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."