src/hg/archaeStuff/scripts/make-browser-2.0 1.49

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 1.48
retrieving revision 1.49
diff -b -B -U 4 -r1.48 -r1.49
--- src/hg/archaeStuff/scripts/make-browser-2.0	22 Sep 2009 22:07:50 -0000	1.48
+++ src/hg/archaeStuff/scripts/make-browser-2.0	6 Oct 2009 17:35:09 -0000	1.49
@@ -18,8 +18,9 @@
 use archaeBrowser::GenomeInfo;
 use archaeBrowser::ConservedDomains;
 use archaeBrowser::ProteinDb;
 use archaeBrowser::OrganismDb;
+use archaeBrowser::RemovePriv;
 use archaeBrowser::Track;
 use archaeBrowser::CDS;
 use archaeBrowser::Blat;
 use archaeBrowser::Blast;
@@ -72,9 +73,9 @@
 
 # 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_generefs,
- $opt_syncg,$opt_synct,$opt_syncd, $opt_syncc, $opt_syncdw, $opt_loaddump, $opt_allorg,$opt_snapshot, $opt_cleanblast,
+ $opt_syncg,$opt_synct,$opt_syncd, $opt_syncc, $opt_syncdw, $opt_loaddump, $opt_allorg,$opt_snapshot, $opt_removepriv,
  $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,
  $opt_arkops, $opt_tigrops, $opt_commit, $opt_perm, $opt_tracksup, $opt_altdb, $opt_primers,
@@ -146,9 +147,9 @@
         next;
     }
 
     if ($opt_loaddump)             { &Load_dbdump(\%global_vars); &Load_desc_page(\%global_vars); }
-    if ($opt_cleanblast)           { &Clean_blast_hits(\%global_vars); }
+    if ($opt_removepriv)           { &Remove_private_genome_hits(\%global_vars); }
     if ($opt_initdb)               { &Initialize_org_db(\%global_vars); }
     if ($opt_syncg)                { &Sync_genome_db(\%global_vars, "public"); }
     if ($opt_synct)                { &Sync_genome_db(\%global_vars, "test"); }
     if ($opt_syncd)                { &Sync_genome_db(\%global_vars, "dev"); }
@@ -200,14 +201,14 @@
 #    if ($opt_wiki)                 { &Load_wiki("wiki", \%global_vars); }
 #    if ($opt_wikibme)              { &Load_wiki("wikibme", \%global_vars); }
     if ($opt_aligntracks)          { &Load_align_genes_track(\%global_vars);   }
     if ($opt_cdd)                  { &Load_Conserved_Domains(\%global_vars)   }
-    if ($opt_blastp)               { &Load_BlastP_track(\%global_vars,"incremental");   }
-    if ($opt_blastpall)            { &Load_BlastP_track(\%global_vars,"full-rescan");   }
-    if ($opt_blastx)               { &Load_igenics(\%global_vars); &Load_BlastX_track(\%global_vars,"incremental");   }
-    if ($opt_blastxall)            { &Load_igenics(\%global_vars); &Load_BlastX_track(\%global_vars,"full-rescan");   }
-    if ($opt_mblastx)              { &Load_mBlastX_track(\%global_vars,"incremental");   }
-    if ($opt_mblastxall)           { &Load_mBlastX_track(\%global_vars,"full-rescan");   }
+    if ($opt_blastp)               { &Load_BlastP_track(\%global_vars,"incremental", 0);  }
+    if ($opt_blastpall)            { &Load_BlastP_track(\%global_vars,"full-rescan", 0);  }
+    if ($opt_blastx)               { &Load_igenics(\%global_vars); &Load_BlastX_track(\%global_vars,"incremental", 0); }
+    if ($opt_blastxall)            { &Load_igenics(\%global_vars); &Load_BlastX_track(\%global_vars,"full-rescan", 0);  }
+    if ($opt_mblastx)              { &Load_mBlastX_track(\%global_vars,"incremental", 0);  }
+    if ($opt_mblastxall)           { &Load_mBlastX_track(\%global_vars,"full-rescan", 0);  }
     if ($opt_predictGenes)         { &PredictGenes(\%global_vars);   }
     if ($opt_commit || $opt_all)   { &CVS_commit(\%global_vars);        }
     if ($opt_tracksup || $opt_all) { &Update_tracks(\%global_vars);     }
     if ($global_constants->Web_links_file() ne '')     { &Print_web_links($organism);   }
@@ -398,9 +399,9 @@
     $opt_auth = '';
     $opt_precomp = '';
     $opt_swissprot = '';
 
-    Getopt::Long::GetOptions("getseqs","joinassembly", "initdb","hidedb","droptable=s","initblat","gc","gbhits","cleanblast",
+    Getopt::Long::GetOptions("getseqs","joinassembly", "initdb","hidedb","droptable=s","initblat","gc","gbhits","removepriv",
                  "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",
@@ -449,9 +450,9 @@
     "            --commit  :  cvs commit changes to description.html front page\n",
     "            --perm    :  Set permissions to group-writeable for all files\n",
     "            --public  :  Required to update public genome server DB\n",
     "            --loaddump:  Load mySql database for organism onto current server (after running --syncg command)\n",
-    "            --cleanblast:  Clean blast hits to genomes that do not exist in centraldb\n",
+    "            --removepriv:  Remove hits to private genomes that do not exist in centraldb\n",
     "            --web=<file>  :  Print web links and image map info using coordinates from <file>\n",
     "            --snapshot <browser addr> :  Save an image snapshot of <browser addr> (i.e. archaea.ucsc.edu)\n",
     "            --auth <user:pass>        :  Used with --snapshot to authorize access to protected sites\n\n",