Merge pull request #4 from algbio/fix-random-path

Fix random path to not repeat ids

Author: elarielcl

src/AlignmentGraph.cpp

@@ -1507,8 +1507,12 @@ std::vector<size_t> AlignmentGraph::generatePath(const std::string &seq_out, con
 }
 std::ofstream fout(seq_out), pout(path_out);
 fout << ">path_" << path[0] << "_" << path.back() << std::endl;
-for (size_t i : path) {
-pout << i << ' ' << nodeIDs[i] << std::endl;
+int last_nodeID = -1; // Assumed not to be a valid ID
+ for (size_t i : path) {
+if (nodeIDs[i] != last_nodeID) {
+	pout << i << ' ' << nodeIDs[i] << std::endl;
+	last_nodeID = nodeIDs[i];
+}
 // std::cout << i << " " << nodeIDs[i] << " " << reverse[i] << " : ";
 for (size_t j = 0; j < NodeLength(i); j++) {
 fout << NodeSequences(i, j);
@@ -1896,4 +1900,4 @@ std::vector<size_t> AlignmentGraph::getChainPath(size_t S, size_t T, long long s
 tmp.push_back(S);
 std::reverse(tmp.begin(), tmp.end());
 return tmp;
-}
+}