5dcb723fb12fbac15ffdd0c3464fce6f722e2e7e
hiram
  Wed Feb 19 13:40:18 2025 -0800
readjust default visibilities refs #35201

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index d24fc1e81e1..2a600ed423d 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -46,51 +46,51 @@
 # check to see if there is a searchTrix assembly index
 if [ -s ${buildDir}/trackData/assemblyGap/${asmId}.assembly.ix ]; then
   rm -f $buildDir/ixIxx/${asmId}.assembly.ix*
   ln -s ../trackData/assemblyGap/${asmId}.assembly.ix $buildDir/ixIxx
   ln -s ../trackData/assemblyGap/${asmId}.assembly.ixx $buildDir/ixIxx
   searchTrix="
 searchTrix ixIxx/${asmId}.assembly.ix"
 fi
 
 if [ -s ${buildDir}/trackData/assemblyGap/${asmId}.assembly.bb ]; then
 rm -f $buildDir/bbi/${asmId}.assembly.bb
 ln -s ../trackData/assemblyGap/${asmId}.assembly.bb $buildDir/bbi/${asmId}.assembly.bb
 printf "track assembly
 longLabel Assembly
 shortLabel Assembly
-visibility pack
+visibility hide
 colorByStrand 150,100,30 230,170,40
 color 150,100,30
 altColor 230,170,40
 bigDataUrl bbi/%s.assembly.bb
 type bigBed 6
 html html/%s.assembly
 searchIndex name%s
 url https://www.ncbi.nlm.nih.gov/nuccore/\$\$
 urlLabel NCBI Nucleotide database:
 group map\n\n" "${asmId}" "${asmId}" "${searchTrix}"
 $scriptDir/asmHubAssembly.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/$asmId.agp.gz https://hgdownload.soe.ucsc.edu/hubs/VGP/genomes/$asmId > $buildDir/html/$asmId.assembly.html
 fi
 
 if [ -s ${buildDir}/trackData/assemblyGap/${asmId}.gap.bb ]; then
 rm -f $buildDir/bbi/${asmId}.gap.bb
 ln -s ../trackData/assemblyGap/${asmId}.gap.bb $buildDir/bbi/${asmId}.gap.bb
 printf "track gap
 longLabel AGP gap
 shortLabel Gap (AGP defined)
-visibility dense
+visibility hide
 color 0,0,0
 bigDataUrl bbi/%s.gap.bb
 type bigBed 4
 group map
 html html/%s.gap\n\n" "${asmId}" "${asmId}"
 $scriptDir/asmHubGap.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/$asmId.agp.gz https://hgdownload.soe.ucsc.edu/hubs/VGP/genomes/$asmId > $buildDir/html/$asmId.gap.html
 fi
 
 if [ -s ${buildDir}/trackData/cytoBand/${asmId}.cytoBand.bb ]; then
 rm -f $buildDir/bbi/${asmId}.cytoBand.bb
 ln -s ../trackData/cytoBand/${asmId}.cytoBand.bb $buildDir/bbi/${asmId}.cytoBand.bb
 
 # printf "track cytoBand
 # shortLabel Chromosome Band
 # longLabel Ideogram
@@ -108,31 +108,31 @@
 group map
 visibility dense
 type bigBed 4 +
 bigDataUrl bbi/%s.cytoBand.bb\n\n" "${asmId}"
 
 # $scriptDir/asmHubCytoBand.pl $asmId $buildDir/html/$asmId.names.tab $buildDir > $buildDir/html/$asmId.cytoBand.html
 fi
 
 if [ -s ${buildDir}/trackData/gc5Base/${asmId}.gc5Base.bw ]; then
 rm -f $buildDir/bbi/${asmId}.gc5Base.bw
 ln -s ../trackData/gc5Base/${asmId}.gc5Base.bw $buildDir/bbi/${asmId}.gc5Base.bw
 printf "track gc5Base
 shortLabel GC Percent
 longLabel GC Percent in 5-Base Windows
 group map
-visibility full
+visibility dense
 autoScale Off
 maxHeightPixels 128:36:16
 graphTypeDefault Bar
 gridDefault OFF
 windowingFunction Mean
 color 0,0,0
 altColor 128,128,128
 viewLimits 30:70
 type bigWig 0 100
 bigDataUrl bbi/%s.gc5Base.bw
 html html/%s.gc5Base\n\n" "${asmId}" "${asmId}"
 
 $scriptDir/asmHubGc5Percent.pl $asmId $buildDir/html/$asmId.names.tab $buildDir > $buildDir/html/$asmId.gc5Base.html
 fi
 
@@ -425,31 +425,31 @@
   rm -f $buildDir/bbi/${asmId}.rModel.align.bb
   rm -f $buildDir/bbi/${asmId}.rModel.bb
   rm -f $buildDir/${asmId}.fa.rModel.align.tsv.gz
   rm -f $buildDir/${asmId}.fa.rModel.join.tsv.gz
   if [ -s "$buildDir/trackData/repeatModeler/${asmId}.rmsk.align.bb" ]; then
     ln -s ../trackData/repeatModeler/${asmId}.rmsk.align.bb $buildDir/bbi/${asmId}.rModel.align.bb
     ln -s trackData/repeatModeler/${asmId}.fa.align.tsv.gz $buildDir/${asmId}.fa.rModel.align.tsv.gz
   fi
   ln -s ../trackData/repeatModeler/${asmId}.rmsk.bb $buildDir/bbi/${asmId}.rModel.bb
   ln -s trackData/repeatModeler/${asmId}.sorted.fa.join.tsv.gz $buildDir/${asmId}.fa.rModel.join.tsv.gz
 
 printf "track repeatModeler
 shortLabel RepeatModeler
 longLabel RepeatModeler Repetitive Elements
 type bigRmsk 9 +
-visibility pack
+visibility hide
 group varRep
 bigDataUrl bbi/%s.rModel.bb\n" "${asmId}"
 if [ -s "$buildDir/bbi/${asmId}.rModel.align.bb" ]; then
   printf "xrefDataUrl bbi/%s.rModel.align.bb\n" "${asmId}"
 fi
 printf "maxWindowToDraw 5000000\n"
 export rModelClassProfile="$buildDir/trackData/repeatModeler/$asmId.rmsk.class.profile.txt"
 if [ -s "${rModelClassProfile}" ]; then
   printf "html html/%s.repeatModeler\n\n" "${asmId}"
   $scriptDir/asmHubRmodelJoinAlign.pl $asmId $buildDir > $buildDir/html/$asmId.repeatModeler.html
 else
   printf "\n"
 fi
 
 else	#	else clause of if [ "${newRmodel}" -gt 0 ]
@@ -730,31 +730,31 @@
 ###################################################################
 # 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
   cpgVis="on"
 fi
 if [ -s ${buildDir}/trackData/cpgIslands/unmasked/${asmId}.cpgIslandExtUnmasked.bb -o -s ${buildDir}/trackData/cpgIslands/masked/${asmId}.cpgIslandExt.bb ]; then
 rm -f ${buildDir}/bbi/${asmId}.cpgIslandExtUnmasked.bb ${buildDir}/bbi/${asmId}.cpgIslandExt.bb
 
 printf "track cpgIslands
 compositeTrack on
 shortLabel CpG Islands
 longLabel CpG Islands (Islands < 300 Bases are Light Green)
 group regulation
-visibility pack
+visibility dense
 type bigBed 4 +
 html html/%s.cpgIslands\n\n" "${asmId}"
 fi
 
 if [ -s ${buildDir}/trackData/cpgIslands/masked/${asmId}.cpgIslandExt.bb ]; then
 ln -s ../trackData/cpgIslands/masked/${asmId}.cpgIslandExt.bb ${buildDir}/bbi/${asmId}.cpgIslandExt.bb
 printf "    track cpgIslandExt
     parent cpgIslands %s
     shortLabel CpG Islands
     longLabel CpG Islands (Islands < 300 Bases are Light Green)
     type bigBed 4 +
     priority 1
     bigDataUrl bbi/%s.cpgIslandExt.bb\n\n" "${cpgVis}" "${asmId}"
 fi
 
@@ -788,31 +788,31 @@
 bigDataUrl bbi/%s.windowMasker.bb
 html html/%s.windowMasker\n\n" "${asmId}" "${asmId}"
 $scriptDir/asmHubWindowMasker.pl $asmId $buildDir/html/$asmId.names.tab $buildDir > $buildDir/html/$asmId.windowMasker.html
 fi
 
 ###################################################################
 # allGaps
 if [ -s ${buildDir}/trackData/allGaps/${asmId}.allGaps.bb ]; then
 rm -f ${buildDir}/bbi/${asmId}.allGaps.bb
 ln -s ../trackData/allGaps/${asmId}.allGaps.bb ${buildDir}/bbi/${asmId}.allGaps.bb
 
 printf "track allGaps
 shortLabel All Gaps
 longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps
 group map
-visibility dense
+visibility hide
 type bigBed 3
 bigDataUrl bbi/%s.allGaps.bb
 html html/%s.allGaps\n\n" "${asmId}" "${asmId}"
 $scriptDir/asmHubAllGaps.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/$asmId.agp.gz https://hgdownload.soe.ucsc.edu/hubs/VGP/genomes/$asmId $buildDir/bbi/$asmId > $buildDir/html/$asmId.allGaps.html
 fi
 
 ###################################################################
 # augustus genes
 if [ -z ${not_augustus+x} ]; then
 
 if [ -s ${buildDir}/trackData/augustus/${asmId}.augustus.bb ]; then
 rm -f ${buildDir}/bbi/${asmId}.augustus.bb
 rm -f ${buildDir}/genes/${asmId}.augustus.gtf.gz
 ln -s ../trackData/augustus/${asmId}.augustus.bb ${buildDir}/bbi/${asmId}.augustus.bb
 if [ -s ${buildDir}/trackData/augustus/${asmId}.augustus.gtf.gz ]; then