5acd42ee6f0f2031ce020ff60a2fd1ffa9d7940a
hiram
  Tue Sep 2 13:49:47 2025 -0700
reset default gene name display on RefSeq gene tracks refs #36206

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index 3613f74ee6a..8820e629e52 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -523,84 +523,84 @@
 group genes
 visibility pack
 type bigBed
 dragAndDrop subTracks
 allButtonPair on
 dataVersion $dataVersion
 html html/%s.refSeqComposite
 priority 2
 
         track ncbiRefSeq
         parent refSeqComposite on
         color 12,12,120
         shortLabel RefSeq All
         type bigGenePred
         urls name2=\"https://www.ncbi.nlm.nih.gov/gene/?term=\$\$\" geneName=\"https://www.ncbi.nlm.nih.gov/gene/\$\$\" geneName2=\"https://www.ncbi.nlm.nih.gov/nuccore/\$\$\"
-        labelFields name,geneName,geneName2
-        defaultLabelFields geneName2
+        labelFields name2,geneName,geneName2
+        defaultLabelFields name2
         searchIndex name
         searchTrix ixIxx/%s.ncbiRefSeq.ix
         bigDataUrl bbi/%s.ncbiRefSeq.bb
         longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*)
         idXref ncbiRefSeqLink mrnaAcc name
         baseColorUseCds given
         baseColorDefault genomicCodons
         priority 1\n\n" "${asmId}" "${asmId}" "${asmId}"
 
   if [ -s ${buildDir}/trackData/ncbiRefSeq/$asmId.ncbiRefSeqCurated.bb ]; then
     rm -f $buildDir/bbi/${asmId}.ncbiRefSeqCurated.bb
     rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqCurated.ix
     rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqCurated.ixx
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqCurated.bb $buildDir/bbi/${asmId}.ncbiRefSeqCurated.bb
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqCurated.ix $buildDir/ixIxx/${asmId}.ncbiRefSeqCurated.ix
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqCurated.ixx $buildDir/ixIxx/${asmId}.ncbiRefSeqCurated.ixx
 
     printf "        track ncbiRefSeqCurated
         color 12,12,120
         parent refSeqComposite on
         shortLabel RefSeq Curated
         longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*)
         type bigGenePred
         urls name2=\"https://www.ncbi.nlm.nih.gov/gene/?term=\$\$\" geneName=\"https://www.ncbi.nlm.nih.gov/gene/\$\$\" geneName2=\"https://www.ncbi.nlm.nih.gov/nuccore/\$\$\"
-        labelFields name,geneName,geneName2
-        defaultLabelFields geneName2
+        labelFields name2,geneName,geneName2
+        defaultLabelFields name2
         searchIndex name
         searchTrix ixIxx/%s.ncbiRefSeqCurated.ix
         idXref ncbiRefSeqLink mrnaAcc name
         bigDataUrl bbi/%s.ncbiRefSeqCurated.bb
         baseColorUseCds given
         baseColorDefault genomicCodons
         priority 2\n\n" "${asmId}" "${asmId}"
   fi
 
   if [ -s ${buildDir}/trackData/ncbiRefSeq/$asmId.ncbiRefSeqPredicted.bb ]; then
     rm -f $buildDir/bbi/${asmId}.ncbiRefSeqPredicted.bb
     rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqPredicted.ix
     rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqPredicted.ixx
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqPredicted.bb $buildDir/bbi/${asmId}.ncbiRefSeqPredicted.bb
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqPredicted.ix $buildDir/ixIxx/${asmId}.ncbiRefSeqPredicted.ix
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqPredicted.ixx $buildDir/ixIxx/${asmId}.ncbiRefSeqPredicted.ixx
 
     printf "        track ncbiRefSeqPredicted
         color 12,12,120
         parent refSeqComposite on
         shortLabel RefSeq Predicted
         longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*)
         type bigGenePred
         urls name2=\"https://www.ncbi.nlm.nih.gov/gene/?term=\$\$\" geneName=\"https://www.ncbi.nlm.nih.gov/gene/\$\$\" geneName2=\"https://www.ncbi.nlm.nih.gov/nuccore/\$\$\"
-        labelFields name,geneName,geneName2
-        defaultLabelFields geneName2
+        labelFields name2,geneName,geneName2
+        defaultLabelFields name2
         searchIndex name
         searchTrix ixIxx/%s.ncbiRefSeqPredicted.ix
         idXref ncbiRefSeqLink mrnaAcc name
         bigDataUrl bbi/%s.ncbiRefSeqPredicted.bb
         baseColorUseCds given
         baseColorDefault genomicCodons
         priority 3\n\n" "${asmId}" "${asmId}"
   fi
 
   if [ -s ${buildDir}/trackData/ncbiRefSeq/$asmId.ncbiRefSeqOther.bb ]; then
     rm -f $buildDir/bbi/${asmId}.ncbiRefSeqOther.bb
     rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqOther.ix
     rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqOther.ixx
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqOther.bb $buildDir/bbi/${asmId}.ncbiRefSeqOther.bb
 rm -f $buildDir/ixIxx/${asmId}.xenoRefGene.ix
@@ -696,56 +696,56 @@
 # check to see if there is a index for ncbiGene
 if [ -s ${buildDir}/trackData/ncbiGene/$asmId.ncbiGene.ix ]; then
   searchTrix="
 searchTrix ixIxx/$asmId.ncbiGene.ix"
 fi
 
 
 if [ -s ${buildDir}/trackData/ncbiGene/$asmId.ncbiGene.bb ]; then
 rm -f $buildDir/bbi/${asmId}.ncbiGene.bb
 rm -f $buildDir/ixIxx/${asmId}.ncbiGene.ix
 rm -f $buildDir/ixIxx/${asmId}.ncbiGene.ixx
 rm -f ${buildDir}/genes/${asmId}.ncbiGene.gtf.gz
 export longLabel="Gene models submitted to NCBI"
 export shortLabel="Gene models"
 if [ "$asmType" = "refseq" ]; then
-  longLabel="NCBI gene predictions"
-  shortLabel="NCBI Genes"
+  longLabel="RefSeq gene predictions from NCBI"
+  shortLabel="NCBI RefSeq"
 fi
 if [ -s ${buildDir}/trackData/ncbiGene/${asmId}.ncbiGene.gtf.gz ]; then
   mkdir -p $buildDir/genes
   ln -s ../trackData/ncbiGene/${asmId}.ncbiGene.gtf.gz $buildDir/genes/${asmId}.ncbiGene.gtf.gz
 fi
 ln -s ../trackData/ncbiGene/$asmId.ncbiGene.bb $buildDir/bbi/${asmId}.ncbiGene.bb
 if [ -s  $buildDir/ixIxx/${asmId}.ncbiGene.ix ]; then
   ln -s ../trackData/ncbiGene/$asmId.ncbiGene.ix $buildDir/ixIxx/${asmId}.ncbiGene.ix
   ln -s ../trackData/ncbiGene/$asmId.ncbiGene.ixx $buildDir/ixIxx/${asmId}.ncbiGene.ixx
 fi
   printf "track ncbiGene
 longLabel $longLabel
 shortLabel $shortLabel
 visibility pack
 color 0,80,150
 altColor 150,80,0
 colorByStrand 0,80,150 150,80,0
 bigDataUrl bbi/%s.ncbiGene.bb
 type bigGenePred
 urls name2=\"https://www.ncbi.nlm.nih.gov/gene/?term=\$\$\" geneName=\"https://www.ncbi.nlm.nih.gov/gene/\$\$\" geneName2=\"https://www.ncbi.nlm.nih.gov/nuccore/\$\$\"
 html html/%s.ncbiGene
 searchIndex name%s
 urlLabel Entrez gene:
-labelFields name,geneName,geneName2
+labelFields geneName,geneName2
 defaultLabelFields geneName2
 group genes\n\n" "${asmId}" "${asmId}" "${searchTrix}"
 
   $scriptDir/asmHubNcbiGene.pl $asmId $ncbiAsmId $buildDir/html/$asmId.names.tab $buildDir/trackData > $buildDir/html/$asmId.ncbiGene.html
 
 haveNcbiGene="yes"
 fi	#	if [ -s ${buildDir}/trackData/ncbiGene/$asmId.ncbiGene.bb ]
 fi	#	if [ "${haveNcbiRefSeq}" = "no" ]
 ###################################################################
 
 ###################################################################
 # CpG Islands composite
 export cpgVis="off"
 # if there is no unmasked track, then set cpgVis to pack
 if [ ! -s ${buildDir}/trackData/cpgIslands/unmasked/${asmId}.cpgIslandExtUnmasked.bb ]; then