bio-velvet 0.4.0 → 0.4.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: b5c57762cbeea6210a80415e335e38894efc69aa
-  data.tar.gz: 9a8aba9cfb9a98b76679b025e0833ca366554e18
+  metadata.gz: 2d61f788902dd64e947b0a072fe7ea4928d0090e
+  data.tar.gz: c74bf34034fed56504e7db21df832117747db1d6
 SHA512:
-  metadata.gz: 7deb192d00d7c4a8461c2e6953a1529ed9b66d2f5191840b71fcbe78d953f1f35c0f807ee62e572af0b6d196e961700d5fb45d1dfa181af054803e3d280478f8
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+  metadata.gz: 771d1e978e005c88e90e1c0f6740491f292d6296f7c32bb353ceab4c32b8d268beac7d81d74aa85d09d373ce1be09e53060ba7f41ff8d5203c0f2042cd13f855
+  data.tar.gz: 7630ace0116ba247f7982779874e5a1c0d94db026afcb07792094a64195e09bdbeaee14f4e27c292434c69a47e27481e95665dab41a043415e7fb415b7ebc797

data/VERSION

@@ -1 +1 @@
-0.4.0
+0.4.2

data/lib/bio-velvet/graph.rb

@@ -197,7 +197,7 @@ module Bio
             passable_nodes.push nodes[arc.begin_node_id]
           end
         end
-        return passable_nodes
+        return passable_nodes.uniq
       end
 
       # Return the adjacent nodes in the graph that connect to the end of a node
@@ -211,7 +211,7 @@ module Bio
             passable_nodes.push nodes[arc.end_node_id]
           end
         end
-        return passable_nodes
+        return passable_nodes.uniq
       end
 
 
@@ -440,14 +440,14 @@ module Bio
           revcom(sequence)
         end
 
-        # Number of nucleotides in this node if this contig length is being added to
-        # another node's length (nodes overlap)
-        def length_alone
-          @ends_of_kmers_of_node.length
-        end
-
         def to_s
-          "Node #{@node_id}: #{@ends_of_kmers_of_node} / #{@ends_of_kmers_of_twin_node}"
+          fwd = @ends_of_kmers_of_node
+          rev = @ends_of_kmers_of_twin_node
+          if @ends_of_kmers_of_node.length > 10
+            fwd = @ends_of_kmers_of_node[0...10]+'..'
+            rev = @ends_of_kmers_of_twin_node[0...10]+'..'
+          end
+          "Node #{@node_id}: #{fwd} / #{rev}"
         end
 
         def inspect

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-velvet
 version: !ruby/object:Gem::Version
-  version: 0.4.0
+  version: 0.4.2
 platform: ruby
 authors:
 - Ben J Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-06-14 00:00:00.000000000 Z
+date: 2014-07-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-logger