src/hg/encode/encodeValidate/doEncodeValidate.pl 1.181

Index: src/hg/encode/encodeValidate/doEncodeValidate.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/encodeValidate/doEncodeValidate.pl,v
retrieving revision 1.180
retrieving revision 1.181
diff -b -B -U 4 -r1.180 -r1.181
--- src/hg/encode/encodeValidate/doEncodeValidate.pl	1 May 2009 06:20:28 -0000	1.180
+++ src/hg/encode/encodeValidate/doEncodeValidate.pl	7 May 2009 19:46:05 -0000	1.181
@@ -1113,9 +1113,9 @@
 $opt_sendEmail = 0 if (!defined $opt_sendEmail);
 if($opt_justFileDb) {
    $opt_skipAll = $opt_quick = $opt_allowReloads =1;
 }
-$quickOpt = " -quick " if defined ($opt_quick);
+$quickOpt = " -quick=100 " if defined ($opt_quick);  # use validateFiles to validate 100 lines
 
 if($opt_skipAll) {
     $opt_skipAutoCreation = $opt_skipOutput = $opt_skipValidateFiles = 1;
 }
@@ -1462,9 +1462,9 @@
 
                     # XXXX gzip before saving to disk?
                     my @cmds;
                     my $sortFiles;
-                    if(defined($alignmentLine->{fragLength})) {
+                    if(defined($alignmentLine->{fragLength}) && $alignmentLine->{fragLength} != 0) {
                         push(@cmds, "/cluster/bin/x86_64/bedExtendRanges $daf->{assembly} $alignmentLine->{fragLength} $files");
                         $sortFiles = " -";
                         # sorting stdin, so have to sort in mem (and control how much mem we use)
                         push @cmds, "sort $SORT_BUF -T $Encode::tempDir -k1,1 -k2,2n $sortFiles";
@@ -1773,15 +1773,16 @@
             print TRACK_RA "    type bed 6\n";
         } else {
             print TRACK_RA "    type $type\n";
         }
-        print TRACK_RA sprintf("    dateSubmitted %04d-%02d-%02d\n", 1900 + $year, $mon + 1, $mday);
-        print TRACK_RA sprintf("    dateUnrestricted %04d-%02d-%02d\n", 1900 + $rYear, $rMon + 1, $rMDay);
-        print TRACK_RA sprintf("    dataVersion %s\n", $Encode::dataVersion);
+        # Obsolete: now in metadata
+        # print TRACK_RA sprintf("    dateSubmitted %04d-%02d-%02d\n", 1900 + $year, $mon + 1, $mday);
+        # print TRACK_RA sprintf("    dateUnrestricted %04d-%02d-%02d\n", 1900 + $rYear, $rMon + 1, $rMDay);
+        # print TRACK_RA sprintf("    dataVersion %s\n", $Encode::dataVersion);
+        # print TRACK_RA $additional;
         if(defined($ddfLine->{accession}) && length($ddfLine->{accession}) > 0) {
             print TRACK_RA sprintf("    accession %s\n",$ddfLine->{accession});
         }
-        print TRACK_RA $additional;
         # metadata proj=wgEncode lab=Yale cell=GM12878 antiBody=Pol2 labVersion="PeakSeq 1.2 ..." dataVersion="ENCODE Feb 2009 Freeze"
         print TRACK_RA sprintf("    metadata %s\n", $metadata);
         print TRACK_RA "\n";
     }