bio-velvet 0.5.0 → 0.6.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 84bcad61582984031f5e34471a84a964c8564485
+  metadata.gz: 953480e0459b37d83bc28cc4de57646835477ba6
+  data.tar.gz: 0fd1add0b0d8e1bcf941f7bf40694be1a68b64af
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+  data.tar.gz: e40b20acd894c260fc352d1516ed3817e90f8e8e0d0609861656d0e626bf440227d5f5c5a25b2869a5bd117c9cf8197b738c564865e8b85c27e746e24f03bfd3

data/VERSION

@@ -1 +1 @@
-0.5.0
+0.6.0

data/lib/bio-velvet/graph.rb

@@ -160,7 +160,7 @@ module Bio
               nr.offset_from_start_of_node = row[1].to_i
               nr.start_coord = row[2].to_i
               nr.direction = current_node_direction
-              current_node.short_reads ||= []
+              current_node.short_reads ||= NodedReadArray.new
               current_node.short_reads.push nr
               next
             end
@@ -271,9 +271,6 @@ module Bio
       end
 
 
-
-
-
       # A container class for a list of Node objects. Can index with 1-offset
       # IDs, so that they line up with the identifiers in velvet Graph files,
       # yet respond sensibly to NodeArray#length, etc.
@@ -373,6 +370,19 @@ module Bio
         end
       end
 
+      class NodedReadArray < Array
+        def get_read_by_id(read_id)
+          # Construct hash if not already done
+          if @read_id_to_short_read_id.nil?
+            @read_id_to_short_read_id = {}
+            each do |short_read|
+              @read_id_to_short_read_id[short_read.read_id] = short_read
+            end
+          end
+          @read_id_to_short_read_id[read_id]
+        end
+      end
+
       class Node
         include Bio::Velvet::Logging
 
@@ -648,7 +658,7 @@ module Bio
               nr.offset_from_start_of_node = row[1].to_i
               nr.start_coord = row[2].to_i
               nr.direction = current_node_direction
-              current_node.short_reads ||= []
+              current_node.short_reads ||= NodedReadArray.new
               current_node.short_reads.push nr
               next
             end

data/spec/graph_spec.rb

@@ -461,4 +461,11 @@ ACTATGCTGGTATTTCACTTCCAGGTACAGG'.gsub(/\n/,''))
     graph.neighbours_into_start(graph.nodes[3]) == [graph.nodes[1]]
     graph.neighbours_into_start(graph.nodes[4]) == []
   end
+
+  it 'should use NodedReadArray' do
+    graph = Bio::Velvet::Graph.parse_from_file File.join(TEST_DATA_DIR, 'short_node_LastGraph')
+    graph.nodes[1].short_reads.kind_of?(Bio::Velvet::Graph::NodedReadArray).should == true
+    first = graph.nodes[1].short_reads[0]
+    graph.nodes[1].short_reads.get_read_by_id(first.read_id).should == first
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-velvet
 version: !ruby/object:Gem::Version
-  version: 0.5.0
+  version: 0.6.0
 platform: ruby
 authors:
 - Ben J Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-01-03 00:00:00.000000000 Z
+date: 2015-01-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-logger