src/hg/encode/encodeValidate/doEncodeValidate.pl 1.201

Index: src/hg/encode/encodeValidate/doEncodeValidate.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/encodeValidate/doEncodeValidate.pl,v
retrieving revision 1.200
retrieving revision 1.201
diff -b -B -U 4 -r1.200 -r1.201
--- src/hg/encode/encodeValidate/doEncodeValidate.pl	9 Oct 2009 23:10:39 -0000	1.200
+++ src/hg/encode/encodeValidate/doEncodeValidate.pl	30 Nov 2009 19:34:05 -0000	1.201
@@ -87,8 +87,10 @@
 options:
     -allowReloads       Allow reloads of existing tables
     -configDir=dir      Path of configuration directory, containing
                         metadata .ra files (default: submission-dir/../config)
+    -database=assembly  Use an assembly other than the default ($assembly); necessary only
+                        when using -validateFile
     -fileType=type	used only with validateFile option; e.g. narrowPeak
     -justFileDb         Just generate the fileDb.ra file which contains all metadata
     -metaDataOnly       Process DAF/DDF and just update the projects.metadata field;
                         equal to -allowReloads -skipAll
@@ -1101,10 +1103,10 @@
 
     if($opt_metaDataOnly) {
         return 0;
     }
-    if($daf->{validationSettings}) {
-        my @set = split('\;', $daf->{validationSettings});
+    if($daf->{validationSettings} || $opt_validateFile) {
+        my @set = $opt_validateFile ? () : split('\;', $daf->{validationSettings});
         if($type eq "validateFiles") {
             my $paramList = "";
             for my $setting (@set) {
                 if($setting =~ /^validateFiles\./) {
@@ -1182,8 +1184,9 @@
                     "validateDaf",
                     "validateFile",
                     "sendEmail",
                     "verbose=i",
+                    "database=s" => \$assembly
                     );
 usage() if (!$ok);
 $opt_verbose = 1 if (!defined $opt_verbose);
 $opt_sendEmail = 0 if (!defined $opt_sendEmail);