88603b198e1787fb26de0479d1782532fbb71b67
hiram
  Tue Jul 23 10:14:37 2019 -0700
added cytoBand navigation refs #23734

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index 2a21dce..587dce0 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -53,49 +53,76 @@
 if [ -s ${buildDir}/trackData/assemblyGap/${asmId}.gap.bb ]; then
 rm -f $buildDir/bbi/${asmId}.gap.bb
 ln -s $buildDir/trackData/assemblyGap/${asmId}.gap.bb $buildDir/bbi/${asmId}.gap.bb
 printf "track gap
 longLabel AGP gap
 shortLabel Gap (AGP defined)
 visibility dense
 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 ../hubs/ncbiAssemblies/$genbankRefseq/$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 $buildDir/trackData/cytoBand/${asmId}.cytoBand.bb $buildDir/bbi/${asmId}.cytoBand.bb
+
+# printf "track cytoBand
+# shortLabel Chromosome Band
+# longLabel Ideogram
+# group map
+# visibility dense
+# type bigBed 4 +
+# bigDataUrl bbi/%s.cytoBandIdeo.bb
+# html html/%s.cytoBand\n\n" "${asmId}" "${asmId}"
+
+# only the ideoGram is needed, not the track
+
+printf "track cytoBandIdeo
+shortLabel Chromosome Band (Ideogram)
+longLabel Ideogram for Orientation
+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 $buildDir/trackData/gc5Base/${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
 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
 
 # see if there are gapOverlap or tandemDup bb files
 export gapOverlapCount=0
 export tanDupCount=0
 if [ -s $buildDir/trackData/gapOverlap/${asmId}.gapOverlap.bb ]; then
   gapOverlapCount=`zcat $buildDir/trackData/gapOverlap/${asmId}.gapOverlap.bed.gz | wc -l`
   rm -f $buildDir/bbi/${asmId}.gapOverlap.bb
   ln -s $buildDir/trackData/gapOverlap/${asmId}.gapOverlap.bb $buildDir/bbi/${asmId}.gapOverlap.bb
 fi
 if [ -s $buildDir/trackData/tandemDups/${asmId}.tandemDups.bb ]; then
   tanDupCount=`zcat $buildDir/trackData/tandemDups/${asmId}.tandemDups.bed.gz | wc -l`
   rm -f $buildDir/bbi/${asmId}.tandemDups.bb
   ln -s $buildDir/trackData/tandemDups/${asmId}.tandemDups.bb $buildDir/bbi/${asmId}.tandemDups.bb