Merge branch 'hotfix/v3.0.1'

cancerit · Jul 7, 2015 · 4168b03 · 4168b03
2 parents 0cf6e9d + ac6ceaf
commit 4168b03
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Showing 6 changed files with 9 additions and 6 deletions.
diff --git a/c++/Makefile b/c++/Makefile
@@ -66,7 +66,7 @@ rearrgroup.o: rearrgroup.cpp rearrgroup.h
 version.inc: ../perl/lib/Bio/Brass.pm
 	perl -I../perl/lib -MBio::Brass -e 'print <<"EOF"'		\
 	  -e '/* Generated from lib/Bio/Brass.pm */'		\
-	  -e '#define BRASS_VERSION "$VERSION"'	\
+	  -e '#define BRASS_VERSION "$$VERSION"'	\
 	  -e 'EOF' > $@
 
 

diff --git a/perl/MYMETA.json b/perl/MYMETA.json
@@ -43,5 +43,5 @@
       }
    },
    "release_status" : "stable",
-   "version" : "v3.0.0"
+   "version" : "v3.0.1"
 }
diff --git a/perl/MYMETA.yml b/perl/MYMETA.yml
@@ -25,4 +25,4 @@ requires:
   Pod::Coverage: '0.23'
   Template: '2.26'
   Test::Fatal: '0.013'
-version: v3.0.0
+version: v3.0.1
diff --git a/perl/bin/combineResults.pl b/perl/bin/combineResults.pl
@@ -39,7 +39,7 @@ sub mergeVcf {
 
   my $new_info = q{##INFO=<ID=BAS,Number=.,Type=Integer,Description="Brass Assembly Score:A maximum score of 100 indicates a perfect pattern of 5 vertices in Velvet's de Bruijn graph">}
                   .qq{\n}
-                  .q{##INFO=<ID=SVCLASS,Number=.,Type=String,Description="basic SV class, deletion, inversion, tandem-duplication">};
+                  .q{##INFO=<ID=SVCLASS,Number=.,Type=String,Description="basic SV class, deletion, inversion, tandem-duplication, translocation">};
   my $new_format = q{##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Count of pairs that span this breakpoint">};
 
   my $info_found = 0;
@@ -188,7 +188,10 @@ sub svclass {
   my ($end_a, $end_b) = @{$_[0]};
   die "Record IDs out of sync at:\n",join("\t",@{$end_a}),"\n",join("\t",@{$end_b}),"\n" if($end_a->[2] !~ m/_[12]$/ || $end_b->[2] !~ m/_[12]$/);
   my $class;
-  if($end_a->[4] =~ m/^[[:upper:]]\[/) {
+  if($end_a->[0] ne $end_b->[0]) {
+    $class = 'translocation';
+  }
+  elsif($end_a->[4] =~ m/^[[:upper:]]\[/) {
     # ++
     $class = 'deletion';
   }

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 = '3.0.0';
+our $VERSION = '3.0.1';
 
 =head1 NAME