8b9550f224b17e9118820b82f88655a589d9e383
hiram
  Tue Apr 6 13:55:04 2021 -0700
eliminate single gapOverlap track and getting ready for lastz chainNet tracks refs #26658

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index 3c63121..7e81501 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -650,48 +650,30 @@
 shortLabel RefSeq mRNAs
 longLabel RefSeq mRNAs mapped to this assembly
 group rna
 visibility pack
 color 180,0,0
 type bigGenePred
 bigDataUrl bbi/%s.xenoRefGene.bb
 labelFields name,geneName,geneName2
 searchIndex name
 searchTrix ixIxx/%s.xenoRefGene.ix
 html html/%s.xenoRefGene\n\n" "${asmId}" "${asmId}" "${asmId}"
 $scriptDir/asmHubXenoRefGene.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/trackData > $buildDir/html/$asmId.xenoRefGene.html
 fi
 
 ###################################################################
-# gapOverlap
-# if [ -s ${buildDir}/trackData/gapOverlap/${asmId}.gapOverlap.bb ]; then
-# rm -f ${buildDir}/bbi/${asmId}.gapOverlap.bb
-# ln -s ../trackData/gapOverlap/${asmId}.gapOverlap.bb ${buildDir}/bbi/${asmId}.gapOverlap.bb
-
-# printf "track gapOverlap
-# shortLabel Gap Overlaps
-# longLabel Exactly identical sequence on each side of a gap
-# group map
-# visibility hide
-# type bigBed 12 .
-# bigDataUrl bbi/%s.gapOverlap.bb
-# html html/%s.gapOverlap\n\n" "${asmId}" "${asmId}"
-
-# $scriptDir/asmHubGapOverlap.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/bbi/$asmId > $buildDir/html/$asmId.gapOverlap.html
-
-# fi
-###################################################################
 # Ensembl genes
 if [ -s ${buildDir}/trackData/ensGene/bbi/${asmId}.ensGene.bb ]; then
 ls -og ${buildDir}/trackData/ensGene/bbi/${asmId}.ensGene.bb 1>&2
 printf "# link: ../trackData/ensGene/bbi/${asmId}.ensGene.bb ${buildDir}/bbi/${asmId}.ensGene.bb\n" 1>&2
 rm -f ${buildDir}/bbi/${asmId}.ensGene.bb
 ln -s ../trackData/ensGene/bbi/${asmId}.ensGene.bb ${buildDir}/bbi/${asmId}.ensGene.bb
 rm -f ${buildDir}/ixIxx/${asmId}.ensGene.ix
 rm -f ${buildDir}/ixIxx/${asmId}.ensGene.ixx
 
 ln -s ../trackData/ensGene/process/${asmId}.ensGene.ix $buildDir/ixIxx/${asmId}.ensGene.ix
 ln -s ../trackData/ensGene/process/${asmId}.ensGene.ixx $buildDir/ixIxx/${asmId}.ensGene.ixx
 
 export ensVersion="v86"
 
 if [ -s ${buildDir}/trackData/ensGene/version.txt ]; then
@@ -712,15 +694,20 @@
 html html/%s.ensGene\n\n" "${ensVersion}" "${asmId}" "${asmId}" "${asmId}"
 
 $scriptDir/asmHubEnsGene.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/bbi/$asmId > $buildDir/html/$asmId.ensGene.html "${ensVersion}"
 
 else
   printf "# no ensGene found\n" 1>&2
 fi
 
 if [ -s ${hubLinks}/${asmId}/rnaSeqData/$asmId.trackDb.txt ]; then
   printf "include rnaSeqData/%s.trackDb.txt\n\n" "${asmId}"
 fi
 
 if [ -s "${buildDir}/$asmId.userTrackDb.txt" ]; then
   printf "include %s.userTrackDb.txt\n\n" "${accessionId}"
 fi
+
+###################################################################
+# check for lastz/chain/net available
+
+# export lz=`ls -d ${buildDir}/trackData/lastz.* 2> /dev/null | wc -l`