src/hg/utils/automation/doBlastzChainNet.pl 1.28
1.28 2009/03/19 16:15:29 hiram
Allow non-split tables, and inclHap option to the blastz pipeline to include haplotypes in the chains
Index: src/hg/utils/automation/doBlastzChainNet.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/automation/doBlastzChainNet.pl,v
retrieving revision 1.27
retrieving revision 1.28
diff -b -B -U 4 -r1.27 -r1.28
--- src/hg/utils/automation/doBlastzChainNet.pl 13 Mar 2009 22:33:13 -0000 1.27
+++ src/hg/utils/automation/doBlastzChainNet.pl 19 Mar 2009 16:15:29 -0000 1.28
@@ -55,8 +55,9 @@
$opt_ignoreSelf
$opt_syntenicNet
$opt_noDbNameCheck
$opt_inclHap
+ $opt_noLoadChainSplit
/;
# Specify the steps supported with -continue / -stop:
my $stepper = new HgStepManager(
@@ -117,8 +118,9 @@
-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
_EOF_
;
print STDERR &HgAutomate::getCommonOptionHelp('dbHost' => $dbHost,
'workhorse' => $workhorse,
@@ -283,9 +285,10 @@
"readmeOnly",
"ignoreSelf",
"syntenicNet",
"noDbNameCheck",
- "inclHap"
+ "inclHap",
+ "noLoadChainSplit"
);
&usage(1) if (!$ok);
&usage(0, 1) if ($opt_help);
&HgAutomate::processCommonOptions();
@@ -964,9 +967,9 @@
$bossScript->add(<<_EOF_
# Load chains:
_EOF_
);
- if ($splitRef) {
+ if ((! $opt_noLoadChainSplit) && $splitRef) {
$bossScript->add(<<_EOF_
cd $runDir/chain
foreach c (`awk '{print \$1;}' $defVars{SEQ1_LEN}`)
set f = \$c.chain