a1691f6b23c5406023f8743fe131af96c5539f18
hiram
  Wed Jul 1 12:40:32 2020 -0700
correct Bob Harris reference for lastz refs #25827

diff --git src/hg/utils/automation/doBlastzChainNet.pl src/hg/utils/automation/doBlastzChainNet.pl
index 7d7d93a..82a34c4 100755
--- src/hg/utils/automation/doBlastzChainNet.pl
+++ src/hg/utils/automation/doBlastzChainNet.pl
@@ -1290,31 +1290,31 @@
 	   "by blastz.\n\n";
     }
     close($fh);
   }
   my $o = $defVars{'BLASTZ_O'} || 400;
   my $e = $defVars{'BLASTZ_E'} || 30;
   my $k = $defVars{'BLASTZ_K'} || 3000;
   my $l = $defVars{'BLASTZ_L'} || 3000;
   my $h = $defVars{'BLASTZ_H'} || 2000;
   my $blastzOther = '';
   foreach my $var (sort keys %defVars) {
     if ($var =~ /^BLASTZ_(\w)$/) {
       my $p = $1;
       if ($p ne 'K' && $p ne 'L' && $p ne 'H' && $p ne 'Q') {
 	if ($blastzOther eq '') {
-	  $blastzOther = 'Other blastz
+	  $blastzOther = 'Other lastz
 parameters specifically set for this species pair:';
 	}
 	$blastzOther .= "\n    $p=$defVars{$var}";
       }
     }
   }
   return ($matrix, $o, $e, $k, $l, $h, $blastzOther);
 }
 
 sub commafy {
   # Assuming $num is a number, add commas where appropriate.
   my ($num) = @_;
   $num =~ s/(\d)(\d\d\d)$/$1,$2/;
   $num =~ s/(\d)(\d\d\d),/$1,$2,/g;
   return($num);
@@ -1496,30 +1496,33 @@
 If you plan to download a large file or multiple files from this directory,
 we recommend you use ftp rather than downloading the files via our website.
 To do so, ftp to hgdownload.soe.ucsc.edu, then go to the directory
 goldenPath/$tDb/vs$QDb/. To download multiple files, use the \"mget\"
 command:
 
     mget <filename1> <filename2> ...
     - or -
     mget -a (to download all files in the current directory)
 
 All files in this directory are freely available for public use.
 
 --------------------------------------------------------------------
 References
 
+Harris, R.S. (2007) Improved pairwise alignment of genomic DNA
+Ph.D. Thesis, The Pennsylvania State University
+
 Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence
 alignments. Pac Symp Biocomput.  2002:115-26.
 
 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.
 Evolution's cauldron: Duplication, deletion, and rearrangement in the
 mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep
 30;100(20):11484-9.
 
 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,
 Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome
 Res. 2003 Jan;13(1):103-7.
 
 ";
   close($fh);
 }