src/hg/utils/automation/doBlastzChainNet.pl 1.31

Index: src/hg/utils/automation/doBlastzChainNet.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/automation/doBlastzChainNet.pl,v
retrieving revision 1.30
retrieving revision 1.31
diff -b -B -U 4 -r1.30 -r1.31
--- src/hg/utils/automation/doBlastzChainNet.pl	26 Oct 2009 20:54:43 -0000	1.30
+++ src/hg/utils/automation/doBlastzChainNet.pl	11 Feb 2010 23:47:51 -0000	1.31
@@ -56,8 +56,9 @@
     $opt_syntenicNet
     $opt_noDbNameCheck
     $opt_inclHap
     $opt_noLoadChainSplit
+    $opt_loadChainSplit
     /;
 
 # Specify the steps supported with -continue / -stop:
 my $stepper = new HgStepManager(
@@ -118,9 +119,9 @@
     -ignoreSelf           Do not assume self alignments even if tDb == qDb
     -syntenicNet          Perform optional syntenicNet step
     -noDbNameCheck        ignore Db name format
     -inclHap              include haplotypes *_hap* in chain/net, default not
-    -noLoadChainSplit     do not load split chain tables even if chrom based
+    -loadChainSplit       load split chain tables, default is not split tables
 _EOF_
   ;
 print STDERR &HgAutomate::getCommonOptionHelp('dbHost' => $dbHost,
 				      'workhorse' => $workhorse,
@@ -286,9 +287,10 @@
 		      "ignoreSelf",
                       "syntenicNet",
                       "noDbNameCheck",
                       "inclHap",
-                      "noLoadChainSplit"
+                      "noLoadChainSplit",
+                      "loadChainSplit"
 		     );
   &usage(1) if (!$ok);
   &usage(0, 1) if ($opt_help);
   &HgAutomate::processCommonOptions();
@@ -517,9 +519,13 @@
   my $bossScript = new HgRemoteScript("$runDir/doPartition.csh", $paraHub,
 				      $runDir, $whatItDoes, $DEF);
   $bossScript->add(<<_EOF_
 $partitionTargetCmd
+set L1 = `wc -l < $targetList`
 $partitionQueryCmd
+set L2 = `wc -l < $queryList`
+set L = `echo \$L1 \$L2 | awk '{print \$1*\$2}'`
+echo "cluster batch jobList size: \$L = \$L1 * \$L1"
 _EOF_
     );
   $bossScript->execute();
   my $mkOutRootHost = $opt_blastzOutRoot ? $paraHub : $fileServer;
@@ -981,9 +987,9 @@
   $bossScript->add(<<_EOF_
 # Load chains:
 _EOF_
     );
-  if ((! $opt_noLoadChainSplit) && $splitRef) {
+  if ($opt_loadChainSplit && $splitRef) {
     $bossScript->add(<<_EOF_
 cd $runDir/chain
 foreach c (`awk '{print \$1;}' $defVars{SEQ1_LEN}`)
     set f = \$c.chain