59737e5bedffc697d6f783c71b56ba711aac7deb
hiram
  Thu Sep 17 12:02:08 2026 -0700
adding loopDetect.sh no redmine

diff --git src/hg/utils/otto/genArk/whatIsNew.sh src/hg/utils/otto/genArk/whatIsNew.sh
index 9b329df598c..beadc85b3b7 100755
--- src/hg/utils/otto/genArk/whatIsNew.sh
+++ src/hg/utils/otto/genArk/whatIsNew.sh
@@ -1,16 +1,22 @@
 #!/bin/bash
+#############################################################################
+###  this script lives in the source tree at:
+###      kent/src/hg/utils/otto/genArk/whatIsNew.sh
+###  edit that copy instead of the in-use copy at:
+###      /hive/data/inside/GenArk/pushRR/whatIsNew.sh
+#############################################################################
 
 export TOP="/hive/data/inside/GenArk/pushRR"
 
 cd "${TOP}"
 
 export doNotCount="public.hub.txt|beta.hub.txt|alpha.hub.txt|user.hub.txt|hub.txt|/contrib/"
 
 export devCount=`zegrep -c -v "${doNotCount}" dev.todayList.gz`
 export betaCount=`zegrep -c -v "${doNotCount}" hgwbeta.todayList.gz`
 export hgw1Count=`zegrep -c -v "${doNotCount}" hgw1.todayList.gz`
 
 printf "### excluding the files:\n\t${doNotCount}\nin these counts.\n"
 
 printf "### count of files on hgwdev: ${devCount}, beta: ${betaCount} and hgw1: ${hgw1Count}\n"
 
@@ -80,17 +86,18 @@
 printf "### files with different time stamps:\n"
 
 rm -f new.timeStamps.txt
 zegrep -v "${doNotCount}" hgwbeta.todayList.gz | sort -k2 \
   | join -t$'\t' -1 2 -2 2 - <(zegrep -v "${doNotCount}" hgw1.todayList.gz | sort -k2) | awk -F$'\t' '$2 != $3' | cut -f1 | sort -u > new.timeStamps.txt
 
 if [ -s "new.timeStamps.txt" ]; then
   head new.timeStamps.txt
   touch rsync.gbdb.genark.fileList.txt rsync.gbdb.toRR.fileList.txt
   cat new.timeStamps.txt >> rsync.gbdb.genark.fileList.txt
   sed -e 's#^#genark/#;'  new.timeStamps.txt >> rsync.gbdb.toRR.fileList.txt
 fi
 
 ./quickLiftNew.sh
 ./liftOverNew.sh
+./loopDetect.sh
 
 exit $?