4fdac1a09cb6a154a2f739885b02fc8f0e40a00d
hiram
  Mon Sep 9 09:57:59 2019 -0700
first instance of hub is complete refs #23734

diff --git src/hg/makeDb/doc/VGP/mkGenomes.pl src/hg/makeDb/doc/VGP/mkGenomes.pl
index 542171a..cc41ab3 100755
--- src/hg/makeDb/doc/VGP/mkGenomes.pl
+++ src/hg/makeDb/doc/VGP/mkGenomes.pl
@@ -40,44 +40,49 @@
   $orgName = $betterName{$asmId} if (exists($betterName{$asmId}));
 
   printf "genome %s\n", $asmId;
   printf "trackDb genomes/%s/%s.trackDb.txt\n", $asmId, $asmId;
   printf "groups groups.txt\n";
   printf "description %s\n", $orgName;
   printf "twoBitPath genomes/%s/%s.2bit\n", $asmId, $asmId;
   printf "organism %s\n", $descr;
   my $chrName=`head -1 $asmId/$asmId.chrom.sizes | awk '{print \$1}'`;
   chomp $chrName;
   my $bigChrom=`head -1 $asmId/$asmId.chrom.sizes | awk '{print \$NF}'`;
   chomp $bigChrom;
   my $oneThird = int($bigChrom/3);
   my $tenK = $oneThird + 10000;
   $tenK = $bigChrom if ($tenK > $bigChrom);
-  printf "defaultPos %s:%d-%d\n", $chrName, $oneThird, $tenK;
+  my $defPos="${chrName}:${oneThird}-${tenK}";
+  if ( -s "$asmId/defaultPos.txt" ) {
+    $defPos=`cat "$asmId/defaultPos.txt"`;
+    chomp $defPos;
+  }
+  printf "defaultPos %s\n", $defPos;
   printf "orderKey %d\n", $orderKey++;
   printf "scientificName %s\n", $descr;
   printf "htmlPath genomes/%s/html/%s.description.html\n", $asmId, $asmId;
   printf "\n";
   my $localGenomesFile = "$asmId/${asmId}.genomes.txt";
   open (GF, ">$localGenomesFile") or die "can not write to $localGenomesFile";
   printf GF "genome %s\n", $asmId;
   printf GF "trackDb %s/%s.trackDb.txt\n", $asmId, $asmId;
   printf GF "groups groups.txt\n";
   printf GF "description %s\n", $orgName;
   printf GF "twoBitPath %s/%s.2bit\n", $asmId, $asmId;
   printf GF "organism %s\n", $descr;
-  printf GF "defaultPos %s:%d-%d\n", $chrName, $oneThird, $tenK;
+  printf GF "defaultPos %s\n", $defPos;
   printf GF "orderKey %d\n", $orderKey++;
   printf GF "scientificName %s\n", $descr;
   printf GF "htmlPath %s/html/%s.description.html\n", $asmId, $asmId;
   close (GF);
 }
 
 __END__
 
 
 description Mastacembelus armatus
 twoBitPath GCA_900324485.2_fMasArm1.2/trackData/addMask/GCA_900324485.2_fMasArm1.2.masked.2bit
 organism Zig-Zag eel
 defaultPos LR535842.1:14552035-14572034
 orderKey 1
 scientificName Mastacembelus armatus