1dea84ee820d50f05255371bdaaf6d7b98f220ca
hiram
  Wed Mar 23 17:03:10 2022 -0700
adding construction of bigBed file for chromAlias refs #29111

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index cb93b70..7cdad79 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -1016,37 +1016,54 @@
 # * step: chromAlias [workhorse]
 sub doChromAlias {
   my $runDir = "$buildDir/trackData/chromAlias";
   &HgAutomate::mustMkdir($runDir);
 
   my $whatItDoes = "construct asmId.chromAlias.txt for alias name recognition";
   my $bossScript = newBash HgRemoteScript("$runDir/doChromAlias.bash",
                     $workhorse, $runDir, $whatItDoes);
 
   $bossScript->add(<<_EOF_
 export buildDir=$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 .
+
 # verify each sequence name has an alias
-export sizeCount=`cat ../../\${asmId}.chrom.sizes | wc -l`
-export aliasCount=`grep -v "^#" \${asmId}.chromAlias.txt | wc -l`
+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
 
 _EOF_
   );
   $bossScript->execute();
 } # chromAlias
 
 #########################################################################
 # * step: gatewayPage [workhorse]
 sub doGatewayPage {
   if ($asmHubName eq "n/a") {
     printf STDERR "ERROR: step gatewayPage needs argument -asmHubName <name>\n";
     exit 255;
   }