src/hg/encode/encodeValidate/doEncodeValidate.pl 1.146

Index: src/hg/encode/encodeValidate/doEncodeValidate.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/encodeValidate/doEncodeValidate.pl,v
retrieving revision 1.145
retrieving revision 1.146
diff -b -B -U 4 -r1.145 -r1.146
--- src/hg/encode/encodeValidate/doEncodeValidate.pl	13 Feb 2009 11:57:04 -0000	1.145
+++ src/hg/encode/encodeValidate/doEncodeValidate.pl	13 Feb 2009 16:17:39 -0000	1.146
@@ -912,10 +912,12 @@
 }
 
 sub validateBowtie
 # Unkown format (for download) from Wold lab. 
-# Sample line:-
+# Sample lines:-
 # HWI-EAS229_75_30DY0AAXX:7:1:0:1545/1    +       chr1    5983615 NCGTCCATCTCACATCGTCAGGAAAGGGGGAAGCACTGGATGGCTGTGGCCTCACAGGCAGGGAGAGTGGGGTCC     IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0       0:G>N
+# HWI-EAS229_75_30DY0AAXX:7:1:0:1591/1      -       uc002fcb.1|22|70699936  45      CTATTTCCACCAAGCAGCCAAGCTCAAGGGAATCGGGGAGTACGTGAACATCCGCACAGGGATGCCCTGCCACTN     IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII     0       0:T>N]
+
 {
     my ($path, $file, $type) = @_;
     doTime("beginning validateBowtie") if $opt_timing;
     my $lineNumber = 0;
@@ -925,9 +927,10 @@
         chomp;
         $lineNumber++;
         next if m/^#/; # allow comment lines, consistent with lineFile and hgLoadBed
         die "Failed bowtie validation, file '$file'; line $lineNumber: line=[$_]\n" 
-	    unless $_ =~ m/^([A-Za-z0-9:>_\/-]+)\t([+-])\t(\w+)\t(\d+)\t(\w+)\t(\w+)\t(\d+)\t([A-Za-z0-9:>_\/-]+)$/;
+	    unless $_ =~ m/^([A-Za-z0-9:>_\|\/-]+)\t([+-])\t([A-Za-z0-9:>_\|\/-]+)\t(\d+)\t(\w+)\t(\w+)\t(\d+)\t([A-Za-z0-9:>_\|\/-]+)$/;
+
         last if($opt_quick && $lineNumber >= $quickCount);
     }
     $fh->close();
     HgAutomate::verbose(2, "File \'$file\' passed $type validation\n");
@@ -957,9 +960,9 @@
         next if $lineNumber == 3 and m/^match/;
         next if $lineNumber == 4 and m/^\s+match/;
         next if $lineNumber == 5 and m/^------/;
         die "Failed $type validation, file '$file'; line $lineNumber: line=[$_]\n" 
-	    unless m/^(\d+)\t(\d+)\t(\d+)\t(\d+)(\d+)\t(\d+)\t(\d+)\t(\d+)\t([+-])\t([A-Za-z0-9:>\/_-]+)\t(\d+)\t(\d+)\t(\d+)\t(\w+)\t(\d+)\t(\d+)\t(\d+)$/;
+	    unless m/^(\d+)\t(\d+)\t(\d+)\t(\d+)(\d+)\t(\d+)\t(\d+)\t(\d+)\t([+-])\t([A-Za-z0-9:>\|\/_-]+)\t(\d+)\t(\d+)\t(\d+)\t(\w+)\t(\d+)\t(\d+)\t(\d+)$/;
         last if($opt_quick && $lineNumber >= $quickCount);
     }
     $fh->close();
     HgAutomate::verbose(2, "File \'$file\' passed $type validation\n");