src/hg/utils/automation/doRepeatMasker.pl 1.14

Index: src/hg/utils/automation/doRepeatMasker.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/automation/doRepeatMasker.pl,v
retrieving revision 1.13
retrieving revision 1.14
diff -b -B -U 4 -r1.13 -r1.14
--- src/hg/utils/automation/doRepeatMasker.pl	5 Feb 2009 16:29:36 -0000	1.13
+++ src/hg/utils/automation/doRepeatMasker.pl	19 Mar 2009 16:15:29 -0000	1.14
@@ -27,8 +27,9 @@
     $opt_buildDir
     $opt_species
     $opt_unmaskedSeq
     $opt_customLib
+    $opt_noSplit
     /;
 
 # Specify the steps supported with -continue / -stop:
 my $stepper = new HgStepManager(
@@ -66,8 +67,9 @@
                           Default: $defaultSpecies.
     -unmaskedSeq seq.2bit Use seq.2bit as the unmasked input sequence instead
                           of default ($unmaskedSeq).
     -customLib lib.fa     Use custom repeat library instead of RepeatMaskers\'s.
+    -noSplit              Do not load split _rmsk tables even if chrom based.
 _EOF_
   ;
   print STDERR &HgAutomate::getCommonOptionHelp('dbHost' => $dbHost,
 						'workhorse' => '',
@@ -108,8 +110,9 @@
 		      'buildDir=s',
 		      'species=s',
 		      'unmaskedSeq=s',
 		      'customLib=s',
+		      'noSplit',
 		      @HgAutomate::commonOptionSpec,
 		      );
   &usage(1) if (!$ok);
   &usage(0, 1) if ($opt_help);
@@ -351,15 +354,17 @@
   my $runDir = "$buildDir";
   &HgAutomate::checkExistsUnlessDebug('cat', 'install', "$buildDir/$db.fa.out");
 
   my $split = $chromBased ? " (split)" : "";
+  $split = "" if ($opt_noSplit);
   my $whatItDoes =
 "It loads $db.fa.out into the$split rmsk table and $db.nestedRepeats.bed\n" .
 "into the nestedRepeats table.  It also installs the masked 2bit.";
   my $bossScript = new HgRemoteScript("$runDir/doLoad.csh", $dbHost,
 				      $runDir, $whatItDoes);
 
   $split = $chromBased ? "-split" : "-nosplit";
+  $split = "-nosplit" if ($opt_noSplit);
   my $installDir = "$HgAutomate::clusterData/$db";
   $bossScript->add(<<_EOF_
 hgLoadOut -table=rmsk $split $db $db.fa.out
 hgLoadBed $db nestedRepeats $db.nestedRepeats.bed \\