src/hg/encode/encodeValidate/doEncodeValidate.pl 1.224

Index: src/hg/encode/encodeValidate/doEncodeValidate.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/encodeValidate/doEncodeValidate.pl,v
retrieving revision 1.223
retrieving revision 1.224
diff -b -B -U 4 -r1.223 -r1.224
--- src/hg/encode/encodeValidate/doEncodeValidate.pl	28 Apr 2010 23:14:08 -0000	1.223
+++ src/hg/encode/encodeValidate/doEncodeValidate.pl	11 May 2010 20:25:02 -0000	1.224
@@ -297,9 +297,8 @@
     rpkm  => \&validateRpkm,
     fasta  => \&validateFasta,
     bowtie  => \&validateBowtie,
     psl  => \&validatePsl,
-    BAM => \&validateBAM,
     cBiP => \&validateFreepass,  # TODO: this is a dodge, because bed file is for different species, so chrom violations
     bigWig => \&validateBigWig,
     bam => \&validateBam,
     );
@@ -791,24 +790,8 @@
     doTime("done validateBigWig") if $opt_timing;
     return ();
 }
 
-sub validateBAM
-{
-    my ($path, $file, $type) = @_;
-    doTime("beginning validateBAM") if $opt_timing;
-    HgAutomate::verbose(2, "validateBAM($path,$file,$type)\n");
-    my $paramList = validationSettings("validateFiles","BAM");
-    my $safe = SafePipe->new(CMDS => ["validateFiles $quickOpt $paramList -type=BAM $file"]);
-    if(my $err = $safe->exec()) {
-	print STDERR  "ERROR: failed validateBAM : " . $safe->stderr() . "\n";
-	# don't show end-user pipe error(s)
-	return("failed validateBAM for '$file'");
-    }
-    HgAutomate::verbose(2, "File \'$file\' passed $type validation\n");
-    doTime("done validateBAM") if $opt_timing;
-    return ();
-}
 
 sub validateCsqual
 {
     # Syntax per http://marketing.appliedbiosystems.com/mk/submit/SOLID_KNOWLEDGE_RD?_JS=T&rd=dm