src/hg/encode/encodeValidate/doEncodeValidate.pl 1.170

Index: src/hg/encode/encodeValidate/doEncodeValidate.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/encodeValidate/doEncodeValidate.pl,v
retrieving revision 1.169
retrieving revision 1.170
diff -b -B -U 4 -r1.169 -r1.170
--- src/hg/encode/encodeValidate/doEncodeValidate.pl	22 Mar 2009 02:37:47 -0000	1.169
+++ src/hg/encode/encodeValidate/doEncodeValidate.pl	26 Mar 2009 07:01:20 -0000	1.170
@@ -29,9 +29,8 @@
 use Carp qw(cluck);
 use Cwd;
 use IO::File;
 use File::Basename;
-use Data::Dumper; # MJP
 
 use lib "/cluster/bin/scripts";
 use Encode;
 use HgAutomate;
@@ -654,9 +653,10 @@
 
 sub validateTagAlign
 {
     my ($path, $file, $type) = @_;
-    my $safe = SafePipe->new(CMDS => ["validateFiles -type=tagAlign $file"]);
+    # validate chroms, chromSize, etc. Assume hg18 like elsewhere
+    my $safe = SafePipe->new(CMDS => ["validateFiles -chromDb=hg18 -type=tagAlign $file"]);
     if(my $err = $safe->exec()) {
 	print STDERR  "ERROR: failed validateTagAlign : " . $safe->stderr() . "\n";
 	# don't show end-user pipe error(s)
 	return("failed validateTagAlign for '$file'");
@@ -667,9 +667,10 @@
 sub validatePairedTagAlign
 # This is like tag align but with two additional sequence fields appended; seq1 and seq2
 {
     my ($path, $file, $type) = @_;
-    my $safe = SafePipe->new(CMDS => ["validateFiles -type=pairedTagAlign $file"]);
+    # validate chroms, chromSize, etc. Assume hg18 like elsewhere
+    my $safe = SafePipe->new(CMDS => ["validateFiles -chromDb=hg18 -type=pairedTagAlign $file"]);
     if(my $err = $safe->exec()) {
 	print STDERR  "ERROR: failed validatePairedTagAlign : " . $safe->stderr() . "\n";
 	# don't show end-user pipe error(s)
 	return("failed validatePairedTagAlign for '$file'");
@@ -695,9 +696,10 @@
 
 sub validateBroadPeak
 {
     my ($path, $file, $type) = @_;
-    my $safe = SafePipe->new(CMDS => ["validateFiles -type=broadPeak $file"]);
+    # validate chroms, chromSize, etc. Assume hg18 like elsewhere
+    my $safe = SafePipe->new(CMDS => ["validateFiles -chromDb=hg18 -type=broadPeak $file"]);
     if(my $err = $safe->exec()) {
 	print STDERR  "ERROR: failed validateBroadPeak : " . $safe->stderr() . "\n";
 	# don't show end-user pipe error(s)
 	return("failed validateBroadPeak for '$file'");