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/mkSymLinks.pl src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
index 57df808..141acac 100755
--- src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
+++ src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
@@ -79,31 +79,33 @@
   printf STDERR "# %03d symlinks %s %s\n", $buildDone, $accessionId, $asmId;
 #  printf STDERR "%s\n", $buildDir;
 #  printf STDERR "%s\n", $destDir;
   if ( ! -d "${destDir}" ) {
     `mkdir -p "${destDir}"`;
   }
   `rm -f "${destDir}/bbi"`;
   `rm -f "${destDir}/genes"`;
   `rm -f "${destDir}/ixIxx"`;
   `rm -f "${destDir}/genesGtf"`;
   `rm -f "${destDir}/liftOver"`;
   `rm -f "${destDir}/otherAligners"`;
   `rm -fr "${destDir}/html"`;
   `mkdir -p "${destDir}/html"`;
   `rm -f "${destDir}/${accessionId}.2bit"`;
+  `rm -f "${destDir}/${accessionId}.chrNames.2bit"`;
   `rm -f "${destDir}/${accessionId}.fa.gz"`;
+  `rm -f "${destDir}/${accessionId}.chrNames.fa.gz"`;
   `rm -f "${destDir}/${accessionId}.2bit.bpt"`;
   `rm -f "${destDir}/${accessionId}.untrans.gfidx"`;
   `rm -f "${destDir}/${accessionId}.trans.gfidx"`;
   `rm -f "${destDir}/${accessionId}.agp.gz"`;
   `rm -f "${destDir}/${accessionId}.chrom.sizes"`;
   `rm -f "${destDir}/${accessionId}.chrom.sizes.txt"`;
   `rm -f "${destDir}/${accessionId}.chromAlias.txt"`;
   `rm -f "${destDir}/${accessionId}.chromAlias.bb"`;
   `rm -f "${destDir}/${accessionId}_assembly_report.txt"`;
   `rm -f "${destDir}/${accessionId}.repeatMasker.out.gz"`;
   `rm -f "${destDir}/${accessionId}.userTrackDb.txt"`;
   `rm -f "${destDir}/trackDb.txt"`;
   `rm -f "${destDir}/genomes.txt"`;
   `rm -f "${destDir}/download.genomes.txt"`;
   `rm -f "${destDir}/hub.txt"`;
@@ -113,31 +115,33 @@
   `ln -s "${buildDir}/genes" "${destDir}/genes"` if (-d "${buildDir}/genes");
   `ln -s "${buildDir}/ixIxx" "${destDir}/ixIxx"` if (-d "${buildDir}/ixIxx");
   `ln -s "${buildDir}/genesGtf" "${destDir}/genesGtf"` if (-d "${buildDir}/genesGtf");
   `ln -s "${buildDir}/liftOver" "${destDir}/liftOver"` if (-d "${buildDir}/liftOver");
   `ln -s "${buildDir}/otherAligners" "${destDir}/otherAligners"` if (-d "${buildDir}/otherAligners");
   `ln -s ${buildDir}/html/*.html "${destDir}/html/"` if (-d "${buildDir}/html");
    my $jpgFiles =`ls ${buildDir}/html/*.jpg 2> /dev/null | wc -l`;
    chomp $jpgFiles;
    if ($jpgFiles > 0) {
     `rm -f ${destDir}/html/*.jpg`;
     `ln -s ${buildDir}/html/*.jpg "${destDir}/html/"`;
    }
 #  `ln -s ${buildDir}/html/*.png "${destDir}/genomes/${asmId}/html/"`;
   `ln -s "${buildDir}/trackData/addMask/${asmId}.masked.2bit" "${destDir}/${accessionId}.2bit"` if (-s "${buildDir}/trackData/addMask/${asmId}.masked.2bit");
   `ln -s "${buildDir}/${asmId}.fa.gz" "${destDir}/${accessionId}.fa.gz"` if (-s "${buildDir}/${asmId}.fa.gz");
+  `ln -s "${buildDir}/${asmId}.chrNames.fa.gz" "${destDir}/${accessionId}.chrNames.fa.gz"` if (-s "${buildDir}/${asmId}.chrNames.fa.gz");
   `ln -s "${buildDir}/trackData/addMask/${asmId}.masked.2bit.bpt" "${destDir}/${accessionId}.2bit.bpt"` if (-s "${buildDir}/trackData/addMask/${asmId}.masked.2bit.bpt");
+  `ln -s "${buildDir}/${asmId}.chrNames.2bit" "${destDir}/${accessionId}.chrNames.2bit"` if (-s "${buildDir}/${asmId}.chrNames.2bit");
    if (-s "${buildDir}/${accessionId}.untrans.gfidx") {
       if (-s "${buildDir}/${accessionId}.trans.gfidx") {
         `ln -s "${buildDir}/${accessionId}.untrans.gfidx" "${destDir}/${accessionId}.untrans.gfidx"`;
         `ln -s "${buildDir}/${accessionId}.trans.gfidx" "${destDir}/${accessionId}.trans.gfidx"`;
       }
    }
   `ln -s "${buildDir}/${asmId}.agp.gz" "${destDir}/${accessionId}.agp.gz"` if (-s "${buildDir}/${asmId}.agp.gz");
   `ln -s "${buildDir}/${asmId}.chrom.sizes" "${destDir}/${accessionId}.chrom.sizes.txt"` if (-s "${buildDir}/${asmId}.chrom.sizes");
   `ln -s "${buildDir}/${asmId}.chromAlias.txt" "${destDir}/${accessionId}.chromAlias.txt"` if (-s "${buildDir}/${asmId}.chromAlias.txt");
   `ln -s "${buildDir}/${asmId}.chromAlias.bb" "${destDir}/${accessionId}.chromAlias.bb"` if (-s "${buildDir}/${asmId}.chromAlias.bb");
   `ln -s "${buildDir}/${asmId}.repeatMasker.out.gz" "${destDir}/${accessionId}.repeatMasker.out.gz"` if (-s "${buildDir}/${asmId}.repeatMasker.out.gz");
   `ln -s "${buildDir}/download/${asmId}_assembly_report.txt" "${destDir}/${accessionId}_assembly_report.txt"` if (-s "${buildDir}/download/${asmId}_assembly_report.txt");
   # trackDb.txt still needed for use by top-level genomes.txt file
   `ln -s "${buildDir}/${asmId}.trackDb.txt" "${destDir}/trackDb.txt"` if (-s "${buildDir}/${asmId}.trackDb.txt");
   # genomes.txt obsolete now with single file