e3dc00ffa75d01a48dfb32178b9d77dab68ee7a5
hiram
  Mon Apr 11 10:00:22 2022 -0700
adding secondary fasta and 2bit delivery and correctly recognize an alternative defaultPosition refs #29203

diff --git src/hg/makeDb/doc/asmHubs/mkGenomes.pl src/hg/makeDb/doc/asmHubs/mkGenomes.pl
index 0bb2b53..5910646 100755
--- src/hg/makeDb/doc/asmHubs/mkGenomes.pl
+++ src/hg/makeDb/doc/asmHubs/mkGenomes.pl
@@ -208,32 +208,32 @@
   # for the chromInfoPage display of hgTracks
   if ( (0 == 1) &&  -s "${buildDir}/${asmId}.chromAlias.bb" ) {
     printf "chromAliasBb ../%s/%s/%s.chromAlias.bb\n", $accessionDir, $accessionId, $accessionId;
   } else {
     printf "chromAlias ../%s/%s/%s.chromAlias.txt\n", $accessionDir, $accessionId, $accessionId;
   }
   printf "organism %s\n", $orgName;
   my $chrName=`head -1 $buildDir/$asmId.chrom.sizes | awk '{print \$1}'`;
   chomp $chrName;
   my $bigChrom=`head -1 $buildDir/$asmId.chrom.sizes | awk '{print \$NF}'`;
   chomp $bigChrom;
   my $oneThird = int($bigChrom/3);
   my $tenK = $oneThird + 10000;
   $tenK = $bigChrom if ($tenK > $bigChrom);
   my $defPos="${chrName}:${oneThird}-${tenK}";
-  if ( -s "$asmId/defaultPos.txt" ) {
-    $defPos=`cat "$asmId/defaultPos.txt"`;
+  if ( -s "$buildDir/defaultPos.txt" ) {
+    $defPos=`cat "$buildDir/defaultPos.txt"`;
     chomp $defPos;
   }
   printf "defaultPos %s\n", $defPos;
   printf "orderKey %d\n", $buildDone;
   printf "scientificName %s\n", $descr;
   printf "htmlPath ../%s/%s/html/%s.description.html\n", $accessionDir, $accessionId, $asmId;
   # until blat server host is ready for hgdownload, avoid these lines
   if ($blatHost ne $downloadHost) {
     if ( -s "${destDir}/$accessionId.trans.gfidx" ) {
       printf "blat $blatHost$blatHostDomain $blatPort dynamic $accessionDir/$accessionId\n";
     printf "transBlat $blatHost$blatHostDomain $blatPort dynamic $accessionDir/$accessionId\n";
       printf "isPcr $blatHost$blatHostDomain $blatPort dynamic $accessionDir/$accessionId\n";
     }
   }
   printf "\n";