can now find pairs of given sequence IDs

.gitignore

@@ -50,3 +50,4 @@ pkg
 # Ignore Gemfile.lock for gems. See http://yehudakatz.com/2010/12/16/clarifying-the-roles-of-the-gemspec-and-gemfile/
 Gemfile.lock
 *.gemspec
+lib/bio-velvet_underground/external/libvelvet.so.1.0

lib/bio-velvet_underground/velvet_underground.rb

@@ -30,6 +30,21 @@ def [](sequence_id)
         def length
           @readset[:readCount]
         end
+
+        def is_second_in_pair?(sequence_id)
+          if sequence_id==0 or sequence_id > @readset[:readCount]
+            raise "Invalid sequence_id #{sequence_id}"
+          end
+          Bio::Velvet::Underground.isSecondInPair @readset, sequence_id-1
+        end
+
+        def pair_id(sequence_id)
+          if is_second_in_pair?(sequence_id)
+            sequence_id-1
+          else
+            sequence_id+1
+          end
+        end
       end
 
       private
@@ -67,6 +82,9 @@ class ReadSet < FFI::Struct
       # TightString *getTightStringInArray(TightString * tString,
       #			   IDnum	 position);
       attach_function :getTightStringInArray, [:pointer, :int32], :pointer
+
+      # boolean isSecondInPair(ReadSet * reads, IDnum index);
+      attach_function :isSecondInPair, [:pointer, :int32], :bool
     end
   end
 end

spec/binary_sequence_store_spec.rb

@@ -24,4 +24,16 @@
       seqs[78]
       }.to raise_error
   end
+
+  it 'should be able to understand mates' do
+    path = File.join TEST_DATA_DIR, '2', 'CnyUnifiedSeq'
+    seqs = Bio::Velvet::Underground::BinarySequenceStore.new path
+    seqs.is_second_in_pair?(1).should == false
+    seqs.is_second_in_pair?(2).should == true
+    seqs.is_second_in_pair?(5).should == false
+    seqs.pair_id(1).should == 2
+    seqs.pair_id(2).should == 1
+    seqs.pair_id(5).should == 6
+    seqs.pair_id(6).should == 5
+  end
 end