src/hg/encode/encodeValidate/doEncodeValidate.pl 1.148

Index: src/hg/encode/encodeValidate/doEncodeValidate.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/encodeValidate/doEncodeValidate.pl,v
retrieving revision 1.147
retrieving revision 1.148
diff -b -B -U 4 -r1.147 -r1.148
--- src/hg/encode/encodeValidate/doEncodeValidate.pl	13 Feb 2009 17:35:43 -0000	1.147
+++ src/hg/encode/encodeValidate/doEncodeValidate.pl	13 Feb 2009 18:21:58 -0000	1.148
@@ -915,8 +915,9 @@
 # Unkown format (for download) from Wold lab. 
 # 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]
+# HWI-EAS229_75_30DY0AAXX:7:1:0:1766/1    -       chr18   72954304        GCAGCCACCAGAAGCGGGAAGAGGTGAAGACAGAGCCTCCTGCAGAGCTCCCACTCTGCCAACGCCTTGACTTTN     IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0       0:G>N,59:T>G
 {
     my ($path, $file, $type) = @_;
     doTime("beginning validateBowtie") if $opt_timing;
     my $lineNumber = 0;
@@ -926,10 +927,9 @@
         chomp;
         $lineNumber++;
         next if m/^#/; # allow comment lines, consistent with lineFile and hgLoadBed
         die "Failed bowtie validation, file '$file'; line $lineNumber: line=[$_]\n" 
-	    unless $_ =~ m/^([A-Za-z0-9:>_\.\|\/-]+)\t([+-])\t([A-Za-z0-9:>_\.\|\/-]+)\t(\d+)\t(\w+)\t(\w+)\t(\d+)\t([A-Za-z0-9:>_\.\|\/-]+)$/;
-
+	    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");