87f551dfb14925f9e7e1d6f23d798fef313fd73c
hiram
  Mon Sep 1 23:25:33 2025 -0700
new chain net construction and update genePred names

diff --git src/hg/utils/automation/asmHubChainNetTrackDb.pl src/hg/utils/automation/asmHubChainNetTrackDb.pl
index 9d66641e9c1..ef461ab02de 100755
--- src/hg/utils/automation/asmHubChainNetTrackDb.pl
+++ src/hg/utils/automation/asmHubChainNetTrackDb.pl
@@ -37,30 +37,31 @@
   $commonName{$gcX} = $comName;
 }
 close ($CN);
 
 open ($CN, "-|", "hgsql -N -e 'select name,organism from dbDb;' hgcentraltest") or die "can not hgsql -N -e 'select name,organism from dbDb;'";
 while (my $line = <$CN>) {
   chomp $line;
   my ($gcX, $comName) = split('\t', $line);
   $comName =~ s/\s\(.*//;
   $commonName{$gcX} = "$comName/${gcX}";
 }
 close ($CN);
 
 `mkdir -p $buildDir/bbi`;
 `mkdir -p $buildDir/liftOver`;
+`mkdir -p $buildDir/quickLift`;
 
 open (DL, "ls -d $buildDir/trackData/lastz.*|") or die "can not list $buildDir/trackData/lastz.*";
 while (my $lastzDir = <DL>) {
   chomp $lastzDir;
   my $queryDb = basename($lastzDir);
   $queryDb =~ s/lastz.//;
   my $Qdb = ucfirst($queryDb);
 #  push @queryList, $queryDb;
   $queryPrio{$queryDb} = 100;
   my $fbTxt = `ls $buildDir/trackData/lastz.${queryDb}/fb.${targetAccession}.chain${Qdb}Link.txt 2> /dev/null`;
   chomp $fbTxt;
   if (-s "${fbTxt}") {
     my $prio = `cut -d' ' -f5 $fbTxt | tr -d '()%'`;
     chomp $prio;
 #    $queryPrio{$queryDb} = sprintf("%d", int((100 - $prio)+0.5));
@@ -261,34 +262,45 @@
 ", $QueryDb, $targetDb, $N, $comName, $comName, $queryDb, $queryAsmName, $queryDate, $queryDb, $targetDb,
      $QueryDb, $targetDb, $QueryDb, $queryDb, $targetDb, $queryPrio{$queryDb};
 
   }
   $N++;
 }
 
 $N = 0;
 $headerOut = 0;
 foreach my $queryDb (@queryList) {
   $comName = $queryDb;
   $comName = $commonName{$queryDb} if (defined($commonName{$queryDb}));
   $QueryDb = ucfirst($queryDb);
 
   if ( -s "$buildDir/trackData/lastz.$queryDb/axtChain/chainLiftOver${QueryDb}.bb" ) {
+    printf STDERR "### $targetDb.chainLiftOver${QueryDb}.bb\n";
     `rm -f $buildDir/bbi/$targetDb.chainLiftOver${QueryDb}.bb`;
     `rm -f $buildDir/bbi/$targetDb.chainLiftOver${QueryDb}Link.bb`;
     `ln -s ../trackData/lastz.$queryDb/axtChain/chainLiftOver${QueryDb}.bb  $buildDir/bbi/$targetDb.chainLiftOver${QueryDb}.bb`;
     `ln -s ../trackData/lastz.$queryDb/axtChain/chainLiftOver${QueryDb}Link.bb  $buildDir/bbi/$targetDb.chainLiftOver${QueryDb}Link.bb`;
+
+    if ( -s "$buildDir/trackData/lastz.$queryDb/axtChain/${targetAccession}.${queryDb}.quick.bb" ) {
+      printf STDERR  "### $targetDb.chainQuickLift${QueryDb}.bb\n";
+      `rm -f $buildDir/quickLift/${queryDb}.bb`;
+      `rm -f $buildDir/quickLift/${queryDb}.link.bb`;
+      `ln -s ../trackData/lastz.$queryDb/axtChain/${targetAccession}.${queryDb}.quick.bb  $buildDir/quickLift/${queryDb}.bb`;
+      `ln -s ../trackData/lastz.$queryDb/axtChain/${targetAccession}.${queryDb}.quickLink.bb  $buildDir/quickLift/${queryDb}.link.bb`;
+    } else {
+      printf STDERR  "### NOT FOUND: $buildDir/trackData/lastz.$queryDb/axtChain/${targetAccession}.${queryDb}.quick.bb\n";
+    }
     if ( $queryDb !~ m/^GC/ ) {
       $queryDate = `hgsql -N -e 'select description from dbDb where name="$queryDb"' hgcentraltest | sed -e 's/ (.*//;'`;
       chomp $queryDate;
     } else {
       ($queryDate, $queryAsmName) = &HgAutomate::hubDateName($queryDb);
     }
 
   if (0 == $headerOut) {
     printf "
     track %sChainNetViewLiftOver
     shortLabel Lift over
     view liftover
     visibility hide
     parent %sChainNet
     spectrum on