0aa6ca4913057168625becbe9dde31c55116272e
hiram
  Tue May 17 16:21:57 2022 -0700
better use of sizesIsBb for alias.bb test generation no redmine

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index 279603f..bed66a8 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -1026,31 +1026,31 @@
 export buildDir=$buildDir
 export asmId=$asmId
 
 \$HOME/kent/src/hg/utils/automation/asmHubChromAlias.pl \\
     \${asmId} | sort > \${asmId}.chromAlias.txt
 
 \$HOME/kent/src/hg/utils/automation/aliasTextToBed.pl \\
   -chromSizes=\$buildDir/\$asmId.chrom.sizes \\
     -aliasText=\${asmId}.chromAlias.txt \\
       -aliasBed=\${asmId}.chromAlias.bed \\
         -aliasAs=\${asmId}.chromAlias.as \\
         -aliasBigBed=\${asmId}.chromAlias.bb
 
 bigBedToBed -header \${asmId}.chromAlias.bb test.chromAlias.bed
 \$HOME/kent/src/hg/utils/automation/aliasBedToCt.pl \\
-  test.chromAlias.bed .
+  test.chromAlias.bed \${asmId}.chromAlias.bb .
 
 # verify each sequence name has an alias
 export sizeCount=`grep -c . ../../\${asmId}.chrom.sizes`
 export aliasCount=`grep -c -v "^#" \${asmId}.chromAlias.txt`
 export testCount=`grep -c -v "^#" test.chromAlias.bed`
 if [ "\${sizeCount}" -ne "\${aliasCount}" ]; then
   printf "ERROR: chromAlias: incorrect number of aliases chromSizes %d > %d aliasCount\\n" "\${sizeCount}" "\${aliasCount}" 1>&2
   exit 255
 fi
 if [ "\${sizeCount}" -ne "\${testCount}" ]; then
   printf "ERROR: chromAlias: incorrect number of aliases chromSizes %d > %d testCount in bigBed file\\n" "\${sizeCount}" "\${testCount}" 1>&2
   exit 255
 fi
 
 exit 0