87bf7cb823cbfa92f36c972b1e4f805e97ab7e3e
hiram
  Mon Jul 22 10:01:43 2019 -0700
correctly cleaning windowMasker refs #23734

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index 9400076..939efcf 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -984,31 +984,31 @@
   my $runDir = "$buildDir/trackData/windowMasker";
 
   &HgAutomate::mustMkdir($runDir);
 
   my $whatItDoes = "run windowMasker procedure";
   my $bossScript = newBash HgRemoteScript("$runDir/doWindowMasker.bash",
                     $workhorse, $runDir, $whatItDoes);
 
   $bossScript->add(<<_EOF_
 export asmId=$asmId
 
 ### if [ ../../\$asmId.unmasked.2bit -nt fb.\$asmId.rmsk.windowmaskerSdust.txt ]; then
 if [ ../../\$asmId.unmasked.2bit -nt faSize.\$asmId.wmsk.sdust.txt ]; then
   \$HOME/kent/src/hg/utils/automation/doWindowMasker.pl -stop=twobit -buildDir=`pwd` -dbHost=$dbHost \\
     -workhorse=$workhorse -unmaskedSeq=$buildDir/\$asmId.unmasked.2bit \$asmId
-  bedInvert.pl ../../\$asmId.chrom.sizes ../allGaps/\$asmId.allGaps.bed \\
+  bedInvert.pl ../../\$asmId.chrom.sizes ../allGaps/\$asmId.allGaps.bed.gz \\
     > not.gap.bed
   bedIntersect -minCoverage=0.0000000014 windowmasker.sdust.bed \\
      not.gap.bed stdout | sort -k1,1  -k2,2n > cleanWMask.bed
   twoBitMask $buildDir/\$asmId.unmasked.2bit cleanWMask.bed \\
     \$asmId.cleanWMSdust.2bit
   twoBitToFa \$asmId.cleanWMSdust.2bit stdout \\
     | faSize stdin > faSize.\$asmId.cleanWMSdust.txt
   zcat ../repeatMasker/\$asmId.sorted.fa.out.gz | sed -e 's/^  *//; /^\$/d;' \\
     | egrep -v "^SW|^score" | awk '{printf "%s\\t%d\\t%d\\n", \$5, \$6-1, \$7}' \\
       | bedSingleCover.pl stdin > rmsk.bed
   intersectRmskWM=`bedIntersect -minCoverage=0.0000000014 cleanWMask.bed \\
     rmsk.bed stdout | bedSingleCover.pl stdin | ave -col=4 stdin \\
      | grep "^total" | awk '{print \$2}' | sed -e 's/.000000//;'`
   chromSize=`ave -col=2 ../../\$asmId.chrom.sizes \\
      | grep "^total" | awk '{print \$2}' | sed -e 's/.000000//;'`