src/hg/utils/automation/makeDownloads.pl 1.20

Index: src/hg/utils/automation/makeDownloads.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/automation/makeDownloads.pl,v
retrieving revision 1.19
retrieving revision 1.20
diff -b -B -U 4 -r1.19 -r1.20
--- src/hg/utils/automation/makeDownloads.pl	3 Mar 2009 21:46:55 -0000	1.19
+++ src/hg/utils/automation/makeDownloads.pl	19 Mar 2009 16:14:35 -0000	1.20
@@ -17,8 +17,10 @@
 # Option variable names:
 use vars @HgAutomate::commonOptionVars;
 use vars @HgStepManager::optionVars;
 use vars qw/
+    $opt_allowMissedTrfs
+    $opt_noChromRoot
     $opt_ignoreRepeatMasker
     /;
 
 # Specify the steps supported with -continue / -stop:
@@ -48,10 +50,13 @@
 ";
   print STDERR $stepper->getOptionHelp();
   print STDERR &HgAutomate::getCommonOptionHelp('dbHost' => $dbHost,
 					'workhorse' => $defaultWorkhorse);
-  print STDERR "    -ignoreRepeatMasker   do not look for RM .out files\n";
-  print STDERR "
+  print STDERR <<_EOF_
+    -allowMissedTrfs      tolerate missing trfMaskChrom/*.bed files
+    -noChromRoot          find RM .out files for chr*_hap in actual hap chrom name
+    -ignoreRepeatMasker   do not look for RM .out files
+
 Automates generation of assembly download files for genome database \$db:
     compress: Create compressed download files, md5sum.txt and README.txt in
               $HgAutomate::clusterData/\$db/goldenPath/*/
     install:  Create links to those files from
@@ -59,9 +64,10 @@
 This will blow away any existing README.txt files and any files that are
 already in bigZips etc.  So if you have added files specially for this
 release (include README.txt sections), and then need to run this again,
 be sure to back them up in a different directory first.
-";
+_EOF_
+  ;
   # Detailed help (-help):
   print STDERR "
 Assumptions:
 1. $HgAutomate::clusterData/\$db/{\$db.2bit,chrom.sizes} are in place.
@@ -82,8 +88,10 @@
 
 sub checkOptions {
   # Make sure command line options are valid/supported.
   my $ok = GetOptions(@HgStepManager::optionSpec,
+		      'allowMissedTrfs',
+		      'noChromRoot',
 		      'ignoreRepeatMasker',
 		      @HgAutomate::commonOptionSpec,
 		      );
   &usage(1) if (!$ok);
@@ -164,12 +172,16 @@
 	push @chromTrfFiles, $trfFile;
       } elsif ($trfFile =~ /chrM\.bed$/) {
 	$trfFudge++;
       } else {
+	if ($opt_allowMissedTrfs) {
+	    $trfFudge++;
+	} else {
 	warn "Missing TRF $trfFile\n";
 	$problems++;
       }
     }
+    }
     if ($problems > 15) {
       warn "A bunch of missing files... stopping here.\n";
       last;
     }
@@ -1027,9 +1039,11 @@
   foreach my $chr (@chroms) {
     my $chrRoot = $chr;
     $chrRoot =~ s/^chr//;
     $chrRoot =~ s/_random$//;
+    if (! $opt_noChromRoot) {
     $chrRoot =~ s/_\w+_hap\d+//;
+    }
     push @{$chromRoots{$chrRoot}}, $chr;
   }
   $chromGz = "chromosomes";
 } else {