Merge branch 'hotfix/v5.3.3'

cancerit · Apr 3, 2017 · 61857a7 · 61857a7
2 parents 6d41c98 + 8005859
commit 61857a7
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Showing 3 changed files with 9 additions and 2 deletions.
diff --git a/perl/bin/combineResults.pl b/perl/bin/combineResults.pl
@@ -243,6 +243,7 @@ sub mergeBedpe {
       push @new, scalar (split /,/, $new[-1]); # 27 # assembled read count
       push @new, @bits[26..44]; # 28-46
     }
+    clean_record(\@new);
     print $FINAL join("\t", @new),"\n";
     $svclass_bkpt_dist{$id} = { 'svclass' => $new[11],
                                 'bkptdist' =>$new[12],};
@@ -254,6 +255,13 @@ sub mergeBedpe {
   return \%svclass_bkpt_dist;
 }
 
+sub clean_record {
+  my $rec = shift;
+  for(0..@{$rec}-1) {
+      $rec->[$_] = '_' unless(defined $rec->[$_]);
+  }
+}
+
 sub svclass_bedpd {
   my ($chrL, $chrH, $strL, $strH) = @_;
   return 'translocation' if($chrL ne $chrH);
@@ -267,4 +275,3 @@ sub svdist_bedpd {
   return -1 if($chrL ne $chrH);
   return abs $startH - $endL;
 }
-
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 = '5.3.2';
+our $VERSION = '5.3.3';
 
 =head1 NAME