src/hg/encode/encodeValidate/doEncodeValidate.pl 1.172

Index: src/hg/encode/encodeValidate/doEncodeValidate.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/encodeValidate/doEncodeValidate.pl,v
retrieving revision 1.171
retrieving revision 1.172
diff -b -B -U 4 -r1.171 -r1.172
--- src/hg/encode/encodeValidate/doEncodeValidate.pl	2 Apr 2009 22:50:33 -0000	1.171
+++ src/hg/encode/encodeValidate/doEncodeValidate.pl	3 Apr 2009 17:16:41 -0000	1.172
@@ -62,8 +62,9 @@
 our $configPath;        # full path of configuration directory
 our $outPath;           # full path of output directory
 our %terms;             # controlled vocabulary
 our $quickCount=100;
+our $quickOpt = "";     # option to pass to validateFiles prog
 our $time0 = time;
 our $timeStart = time;
 our %chromInfo;         # chromInfo from assembly for chrom validation
 our $maxBedRows=80_000_000; # number of rows to allow in a bed-type file
@@ -654,9 +655,9 @@
 sub validateTagAlign
 {
     my ($path, $file, $type) = @_;
     # validate chroms, chromSize, etc. Assume hg18 like elsewhere
-    my $safe = SafePipe->new(CMDS => ["validateFiles -chromDb=hg18 -type=tagAlign $file"]);
+    my $safe = SafePipe->new(CMDS => ["validateFiles $quickOpt -chromDb=hg18 -type=tagAlign $file"]);
     if(my $err = $safe->exec()) {
 	print STDERR  "ERROR: failed validateTagAlign : " . $safe->stderr() . "\n";
 	# don't show end-user pipe error(s)
 	return("failed validateTagAlign for '$file'");
@@ -668,9 +669,9 @@
 # This is like tag align but with two additional sequence fields appended; seq1 and seq2
 {
     my ($path, $file, $type) = @_;
     # validate chroms, chromSize, etc. Assume hg18 like elsewhere
-    my $safe = SafePipe->new(CMDS => ["validateFiles -chromDb=hg18 -type=pairedTagAlign $file"]);
+    my $safe = SafePipe->new(CMDS => ["validateFiles $quickOpt -chromDb=hg18 -type=pairedTagAlign $file"]);
     if(my $err = $safe->exec()) {
 	print STDERR  "ERROR: failed validatePairedTagAlign : " . $safe->stderr() . "\n";
 	# don't show end-user pipe error(s)
 	return("failed validatePairedTagAlign for '$file'");
@@ -697,9 +698,9 @@
 sub validateBroadPeak
 {
     my ($path, $file, $type) = @_;
     # validate chroms, chromSize, etc. Assume hg18 like elsewhere
-    my $safe = SafePipe->new(CMDS => ["validateFiles -chromDb=hg18 -type=broadPeak $file"]);
+    my $safe = SafePipe->new(CMDS => ["validateFiles $quickOpt -chromDb=hg18 -type=broadPeak $file"]);
     if(my $err = $safe->exec()) {
 	print STDERR  "ERROR: failed validateBroadPeak : " . $safe->stderr() . "\n";
 	# don't show end-user pipe error(s)
 	return("failed validateBroadPeak for '$file'");
@@ -741,9 +742,9 @@
     # - fastq produced directly from Solexa has a 'solexa' quality score
     # - fastq defined by Sanger has a 'PHRED' quality score
     # - The 2 urls above show how to convert between both
     my ($path, $file, $type) = @_;
-    my $safe = SafePipe->new(CMDS => ["validateFiles -type=fastq $file"]);
+    my $safe = SafePipe->new(CMDS => ["validateFiles $quickOpt -type=fastq $file"]);
     if(my $err = $safe->exec()) {
 	print STDERR  "ERROR: failed validateFastQ : " . $safe->stderr() . "\n";
 	# don't show end-user pipe error(s)
 	return("failed validateFastQ for '$file'");
@@ -848,9 +849,9 @@
 {
     my ($path, $file, $type) = @_;
     doTime("beginning validateFasta") if $opt_timing;
     HgAutomate::verbose(2, "validateFasta($path,$file,$type)\n");
-    my $safe = SafePipe->new(CMDS => ["validateFiles -type=fasta $file"]);
+    my $safe = SafePipe->new(CMDS => ["validateFiles $quickOpt -type=fasta $file"]);
     if(my $err = $safe->exec()) {
 	print STDERR  "ERROR: failed validateFasta : " . $safe->stderr() . "\n";
 	# don't show end-user pipe error(s)
 	return("failed validateFasta for '$file'");
@@ -1138,8 +1139,9 @@
                     );
 usage() if (!$ok);
 $opt_verbose = 1 if (!defined $opt_verbose);
 $opt_sendEmail = 0 if (!defined $opt_sendEmail);
+$quickOpt = " -quick " if defined ($opt_quick);
 
 if($opt_skipAll) {
     $opt_skipAutoCreation = $opt_skipOutput = $opt_skipValidateFiles = 1;
 }