d20e29ad88a98f2ee349187337549aa047dc8343
hiram
  Fri Oct 17 12:41:00 2025 -0700
more efficient featureBits measure and show featureBits result in output refs #35575

diff --git src/hg/makeDb/doc/asmHubs/quickLiftCatchUp.sh src/hg/makeDb/doc/asmHubs/quickLiftCatchUp.sh
index 3ea9900d8b8..2c6e9fafce4 100755
--- src/hg/makeDb/doc/asmHubs/quickLiftCatchUp.sh
+++ src/hg/makeDb/doc/asmHubs/quickLiftCatchUp.sh
@@ -146,33 +146,35 @@
 else
   printf "DONE: ${targetAcc}.${queryAcc}.quick.bb\n"
 fi
 
 if [ ${targetAcc}.${queryAcc}.quick.link.txt -nt ${targetAcc}.${queryAcc}.quickLink.bb ]; then
   bedToBigBed -type=bed4+1 -as=$HOME/kent/src/hg/lib/bigLink.as \
    -tab ${targetAcc}.${queryAcc}.quick.link.txt \
     "${querySizes}" \
         ${targetAcc}.${queryAcc}.quickLink.bb
   touch -r ${targetAcc}.${queryAcc}.quick.link.txt ${targetAcc}.${queryAcc}.quickLink.bb
 else
   printf "DONE: ${targetAcc}.${queryAcc}.quickLink.bb\n"
 fi
 
 export totalBases=`ave -col=2 "${querySizes}" | grep "^total" | awk '{printf "%d", $2}'`
-export basesCovered=`bedSingleCover.pl ${targetAcc}.${queryAcc}.quick.link.txt | ave -col=4 stdin | grep "^total" | awk '{printf "%d", $2}'`
+export basesCovered=`bigBedInfo ${targetAcc}.${queryAcc}.quickLink.bb | grep basesCovered | cut -d' ' -f2 | tr -d ','`
 export percentCovered=`echo $basesCovered $totalBases | awk '{printf "%.3f", 100.0*$1/$2}'`
 printf "%d bases of %d (%s%%) in intersection\n" "$basesCovered" "$totalBases" "$percentCovered" > "${fbTargetQuery}"
+printf "# %s %s %s\n" "${targetAcc}" "${queryAcc}" "`cat ${fbTargetQuery}`" 1>&2
+rm -f ${targetAcc}.${queryAcc}.quick.chain.txt ${targetAcc}.${queryAcc}.quick.link.txt
 
 if [[ $target == GC* ]]; then
     cd "${targetDir}"
     cd ..
     ./doTrackDb.bash
     /cluster/home/hiram/kent/src/hg/utils/automation/addQuickLift.py \
       "${targetAcc}" "${queryAcc}" "${quickLinkPath}.bb"
 else
     printf "/cluster/home/hiram/kent/src/hg/utils/automation/addQuickLift.py ${targetAcc} ${queryAcc} ${quickLinkPath}.bb\n" 1>&2
     /cluster/home/hiram/kent/src/hg/utils/automation/addQuickLift.py ${targetAcc} ${queryAcc} ${quickLinkPath}.bb
     printf "ln -s ${quickLinkSrc}.quick.bb ${quickLinkPath}.bb\n"
     printf "ln -s ${quickLinkSrc}.quickLink.bb ${quickLinkPath}.link.bb\n"
     ln -s ${quickLinkSrc}.quick.bb ${quickLinkPath}.bb
     ln -s ${quickLinkSrc}.quickLink.bb ${quickLinkPath}.link.bb
 fi