src/hg/archaeStuff/scripts/make-browser-2.0 1.45

Index: src/hg/archaeStuff/scripts/make-browser-2.0
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/archaeStuff/scripts/make-browser-2.0,v
retrieving revision 1.44
retrieving revision 1.45
diff -b -B -U 4 -r1.44 -r1.45
--- src/hg/archaeStuff/scripts/make-browser-2.0	3 Aug 2009 20:32:51 -0000	1.44
+++ src/hg/archaeStuff/scripts/make-browser-2.0	14 Aug 2009 17:31:02 -0000	1.45
@@ -71,9 +71,9 @@
 
 
 # Program option variables
 our ($opt_getseqs, $opt_joinassembly, $opt_initdb, $opt_hidedb, $opt_droptable, $opt_initblat, $opt_gc, $opt_repeats, $opt_iselements,
- $opt_desc, $opt_info, $opt_pfam, $opt_scanpfam, $opt_swissprot, $opt_pfamdesc, $opt_igenics,
+ $opt_desc, $opt_info, $opt_pfam, $opt_scanpfam, $opt_swissprot, $opt_pfamdesc, $opt_igenics,$opt_generefs,
  $opt_syncg,$opt_synct,$opt_syncd, $opt_syncc, $opt_syncdw, $opt_loaddump, $opt_allorg,$opt_snapshot, $opt_cleanblast,
  $opt_genes, $opt_gbhits, $opt_genepred, $opt_cogs, $opt_kegg, $opt_gbrnas, $opt_trnas, $opt_snornas,$opt_auth,
  $opt_rfam, $opt_tigr, $opt_jgi, $opt_easy, $opt_startblat, $opt_killblat, $opt_blatscript, $opt_selfz, $opt_multiz, $opt_ultracons,
  $opt_plfold, $opt_pldensity, $opt_custwig, $opt_wiki, $opt_wikibme, $opt_promsd, $opt_term, $opt_stringdb,
@@ -132,8 +132,9 @@
     $utils->ResetError();
     $utils->org_name($organism->org_name());
 
     if ($opt_info)                 { $organism->Print_org_info($global_constants->gbdb_dir(), $global_constants->Supported_organisms());  }
+    if ($opt_generefs)             { &Dump_generefs(\%global_vars); }
     if ($opt_getseqs)              { &Copy_seqs(\%global_vars); }
     if ($opt_joinassembly)         { &Join_assemblies(\%global_vars); }
     if ($opt_hidedb)               { &Hide_org_db(\%global_vars); }
     if ($opt_droptable ne '')      { &Drop_org_table(\%global_vars, $opt_droptable); }
@@ -385,9 +386,9 @@
     $opt_precomp = '';
     $opt_swissprot = '';
 
     Getopt::Long::GetOptions("getseqs","joinassembly", "initdb","hidedb","droptable=s","initblat","gc","gbhits","cleanblast",
-                 "repeats","iselements", "desc","info",
+                 "repeats","iselements", "desc","info","generefs",
                  "pfam","scanpfam",
                  "genes","genepred","cogs","kegg","gbrnas","trnas","snornas","delete=s", "igenics",
                  "syncg","synct","syncd","syncc","syncdw","loaddump", "swissprot=s", "pfamdesc",
                  "rfam","tigr","jgi","easy","startblat","killblat","blatscript","selfz","multiz", "ultracons",