463d8ccfcc27e9ea403fbf2ed74c344bfbf3897c
hiram
  Wed May 18 13:10:50 2022 -0700
correct if statements to separate the two types of RM tracks no redmine

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index 8235c33..d0803f2 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -193,63 +193,63 @@
 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
+  rm -f $buildDir/${asmId}.fa.align.tsv.gz
+  rm -f $buildDir/${asmId}.fa.join.tsv.gz
   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
+else	#	if [ "${newRmsk}" -eq 2 ]; then
 
 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
 rm -f $buildDir/bbi/${asmId}.rmsk.LINE.bb
@@ -335,30 +335,33 @@
     bigDataUrl bbi/%s.rmsk.RNA.bb\n\n" "${asmId}"
 fi
 
 if [ -s ${buildDir}/trackData/repeatMasker/bbi/${asmId}.rmsk.Other.bb ]; then
 rm -f $buildDir/bbi/${asmId}.rmsk.Other.bb
 ln -s ../trackData/repeatMasker/bbi/${asmId}.rmsk.Other.bb $buildDir/bbi/${asmId}.rmsk.Other.bb
 printf "    track repeatMaskerOther
     parent repeatMasker
     shortLabel Other
     longLabel Other Repeating Elements by RepeatMasker
     type bigBed 6 +
     priority 9
     bigDataUrl bbi/%s.rmsk.Other.bb\n\n" "${asmId}"
 fi
 
+fi	#	if [ "${newRmsk}" -eq 2 ]; then
+fi      #       if [ "${newRmsk}" -eq 2 -o "${rmskCount}" -gt 0 ]; then
+
 if [ -s ${buildDir}/trackData/simpleRepeat/simpleRepeat.bb ]; then
 rm -f $buildDir/bbi/${asmId}.simpleRepeat.bb
 ln -s ../trackData/simpleRepeat/simpleRepeat.bb $buildDir/bbi/${asmId}.simpleRepeat.bb
 printf "track simpleRepeat
 shortLabel Simple Repeats
 longLabel Simple Tandem Repeats by TRF
 group varRep
 visibility dense
 type bigBed 4 +
 bigDataUrl bbi/%s.simpleRepeat.bb
 html html/%s.simpleRepeat\n\n" "${asmId}" "${asmId}"
 $scriptDir/asmHubSimpleRepeat.pl $asmId $buildDir/html/$asmId.names.tab $buildDir > $buildDir/html/$asmId.simpleRepeat.html
 fi
 
 ### assume there is no ncbiRefSeq track