61dccdb3f1405aeee1c397b5247e673cab010911
max
  Thu Dec 14 05:02:54 2023 -0800
adding version.txt files to clinvar. Also starting work on the --alpha
switch, but not tested yet

diff --git src/hg/utils/otto/clinvar/doUpdate.sh src/hg/utils/otto/clinvar/doUpdate.sh
index 442b649..a56d13d 100755
--- src/hg/utils/otto/clinvar/doUpdate.sh
+++ src/hg/utils/otto/clinvar/doUpdate.sh
@@ -1,11 +1,14 @@
 #!/bin/bash
 set -o errexit -o pipefail
 export PATH=$PATH:/cluster/bin/x86_64/ # for bedSort and bedToBigBed
 cd /hive/data/outside/otto/clinvar/
-if [ "$1" == "-nocheck" ]; then
+if [ "$1" == "--alpha" ]; then
+        ./clinVarToBed --auto --alpha
+        ./clinvarSubLolly 0 --alpha
+elif [ "$1" == "-nocheck" ]; then
         ./clinVarToBed --auto
         ./clinvarSubLolly 0 
 else
         ./clinVarToBed --auto --maxDiff 0.1
         ./clinvarSubLolly 0.1
 fi