Handle data that may appear silent for rearrangments

cancerit · Mar 8, 2017 · d86a38f · d86a38f
1 parent 845e98e
commit d86a38f
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Showing 5 changed files with 8 additions and 6 deletions.
diff --git a/perl/docs.tar.gz b/perl/docs.tar.gz
diff --git a/perl/lib/Bio/Brass.pm b/perl/lib/Bio/Brass.pm
@@ -46,7 +46,7 @@ our @EXPORT = qw(find_breakpoints find_dusty_vertices
 		 is_dusty get_isolated_bp_alignment get_isolated_bp_surrounding_region
 		 $VERSION);
 
-our $VERSION = '5.3.1';
+our $VERSION = '5.3.2';
 
 =head1 NAME
 

diff --git a/perl/lib/Sanger/CGP/Brass/Implement.pm b/perl/lib/Sanger/CGP/Brass/Implement.pm
@@ -452,8 +452,8 @@ sub filter {
     sleep 5;
   }
 
-  my $r4_lines = count_lines($abs_bkp_file);
-  my $r5scr_lines = count_lines($score_file);
+  my $r4_lines = count_lines($abs_bkp_file, 1);
+  my $r5scr_lines = count_lines($score_file, 1);
 
   die "Line count mismatch: $abs_bkp_file ($r4_lines) vs $score_file ($r5scr_lines)\n" if($r4_lines != $r5scr_lines);
 
@@ -483,7 +483,8 @@ sub filter {
 }
 
 sub count_lines {
-  my ($file) = @_;
+  my ($file, $allow_no_file) = @_;
+  return 0 if($allow_no_file && ! -e $file);
   open my $FH, '<', $file or die $!;
   while(<$FH>){}
   my $lines = $.;

diff --git a/perl/lib/Sanger/CGP/BrassFilter/BrassMarkedGroups.pm b/perl/lib/Sanger/CGP/BrassFilter/BrassMarkedGroups.pm
@@ -510,8 +510,7 @@ sub process {
   close $self->{bedpe_out_fh} if ($self->{bedpe_out_fh});
 
   unless ($count || ($chunk > 1)) {
-	  print "NO ENTRIES PRINTED. EXITING\n";
-	  exit;
+	  warn "NO ENTRIES PRINTED.\n";
   }
 
   return($count);

diff --git a/perl/lib/Sanger/CGP/BrassFilter/Cleanup.pm b/perl/lib/Sanger/CGP/BrassFilter/Cleanup.pm
@@ -138,6 +138,8 @@ sub process {
     $end_occ_count++;
   }
 
+  $counts{'Groups Total'} ||= 0;
+
   $counts{'Discard - EndOcc'} = $counts{'Groups Total'} - $end_occ_count;
 
   my $col_max = (scalar (keys %name_by_loc))-1;