7c934496e3650521dc129b65658326d542cbd20b
hiram
  Tue May 17 12:52:51 2022 -0700
trying out new rmsk format bigBed joined display no redmine

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index b246373..8235c33 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -174,53 +174,81 @@
     shortLabel Tandem Dups
     longLabel Paired exactly identical sequence survey over entire genome assembly
     bigDataUrl bbi/%s.tandemDups.bb
     type bigBed 12\n\n" "${asmId}"
   fi
 
   $scriptDir/asmHubTanDups.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/trackData > $buildDir/html/$asmId.tanDups.html
 
   else
     printf "# skipping the tanDups track\n" 1>&2
   fi	#	the else clause of: if [ -z ${not_tanDups+x} ]
 fi	#	if [ "${gapOverlapCount}" -gt 0 -o "${tanDupCount}" -gt 0 ]
 
 # see if there are repeatMasker bb files
 export rmskCount=`(ls $buildDir/trackData/repeatMasker/bbi/${asmId}.rmsk.*.bb 2> /dev/null | wc -l) || true`
+export newRmsk=`(ls $buildDir/trackData/repeatMasker/${asmId}.rmsk.align.bb $buildDir/trackData/repeatMasker/${asmId}.rmsk.bb 2> /dev/null | wc -l) || true`
 
-if [ "${rmskCount}" -gt 0 ]; then
+if [ "${newRmsk}" -eq 2 -o "${rmskCount}" -gt 0 ]; then
 
 if [ ! -s "$buildDir/trackData/repeatMasker/$asmId.sorted.fa.out.gz" ]; then
   printf "ERROR: can not find trackData/repeatMasker/$asmId.sorted.fa.out.gz\n" 1>&2
   exit 255
 fi
 
 rm -f $buildDir/$asmId.repeatMasker.out.gz
 ln -s trackData/repeatMasker/$asmId.sorted.fa.out.gz $buildDir/$asmId.repeatMasker.out.gz
+if [ -s "$buildDir/trackData/repeatMasker/versionInfo.txt" ]; then
+   rm -f "$buildDir/${asmId}.repeatMasker.version.txt"
+   ln -s trackData/repeatMasker/versionInfo.txt "$buildDir/${asmId}.repeatMasker.version.txt"
+fi
+
+if [ "${newRmsk}" -eq 2 ]; then
+  rm -f $buildDir/bbi/${asmId}.rmsk.align.bb
+  rm -f $buildDir/bbi/${asmId}.rmsk.bb
+  ln -s ../trackData/repeatMasker/${asmId}.rmsk.align.bb $buildDir/bbi/${asmId}.rmsk.align.bb
+  ln -s ../trackData/repeatMasker/${asmId}.rmsk.bb $buildDir/bbi/${asmId}.rmsk.bb
+  ln -s trackData/repeatMasker/${asmId}.fa.align.tsv.gz $buildDir/${asmId}.fa.align.tsv.gz
+  ln -s trackData/repeatMasker/${asmId}.sorted.fa.join.tsv.gz $buildDir/${asmId}.fa.join.tsv.gz
+
+printf "track repeatMasker
+shortLabel RepeatMasker
+longLabel RepeatMasker Repetitive Elements
+type bigRmsk 9 +
+visibility pack
+group varRep
+bigDataUrl bbi/%s.rmsk.bb
+xrefDataUrl bbi/%s.rmsk.align.bb
+html html/%s.repeatMasker\n\n" "${asmId}" "${asmId}" "${asmId}"
+$scriptDir/asmHubRmskJoinAlign.pl $asmId $buildDir > $buildDir/html/$asmId.repeatMasker.html
+
+else
 
 printf "track repeatMasker
 compositeTrack on
 shortLabel RepeatMasker
 longLabel Repeating Elements by RepeatMasker
 group varRep
 visibility dense
 type bigBed 6 +
 colorByStrand 50,50,150 150,50,50
 maxWindowToDraw 10000000
 spectrum on
 html html/%s.repeatMasker\n\n" "${asmId}"
 $scriptDir/asmHubRmsk.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/trackData/repeatMasker/$asmId.rmsk.class.profile.txt > $buildDir/html/$asmId.repeatMasker.html
+fi
+
 fi      #       if [ "${rmskCount}" -gt 0 ]; then
 
 if [ -s ${buildDir}/trackData/repeatMasker/bbi/${asmId}.rmsk.SINE.bb ]; then
 rm -f $buildDir/bbi/${asmId}.rmsk.SINE.bb
 ln -s ../trackData/repeatMasker/bbi/${asmId}.rmsk.SINE.bb $buildDir/bbi/${asmId}.rmsk.SINE.bb
 printf "    track repeatMaskerSINE
     parent repeatMasker
     shortLabel SINE
     longLabel SINE Repeating Elements by RepeatMasker
     type bigBed 6 +
     priority 1
     bigDataUrl bbi/%s.rmsk.SINE.bb\n\n" "${asmId}"
 fi
 
 if [ -s ${buildDir}/trackData/repeatMasker/bbi/${asmId}.rmsk.LINE.bb ]; then