feat: barcode support to the string graph

chungongyu · Nov 9, 2020 · 1d34045 · 1d34045
1 parent 418d727
commit 1d34045
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Showing 3 changed files with 7 additions and 3 deletions.
diff --git a/src/bigraph.cpp b/src/bigraph.cpp
@@ -503,7 +503,7 @@ bool Bigraph::load(std::istream& stream, size_t minOverlap, bool allowContainmen
  LOG4CXX_ERROR(logger, boost::format("Error: Unexpected vertex record found at line %s") % line);
  return false;
  }
- Vertex* vertex = new Vertex(record.id, record.seq, record.substring ? (int)record.substring : false);
+ Vertex* vertex = new Vertex(record.id, record.seq, record.substring ? (int)record.substring : false, record.barcode ? (std::string)record.barcode : "");
  if (!g->addVertex(vertex)) {
  LOG4CXX_ERROR(logger, boost::format("Error: Attempted to insert vertex into graph with a duplicate id: %s") % vertex->id());
  LOG4CXX_ERROR(logger, "All reads must have a unique identifier");

diff --git a/src/bigraph.h b/src/bigraph.h
@@ -111,7 +111,7 @@ class Vertex {
 public:
  typedef std::string Id;
 
- Vertex(const Id& id, const std::string& seq, bool contained = false) : _id(id), _seq(seq), _contained(contained), _color(GC_NONE), _coverage(1) {
+ Vertex(const Id& id, const std::string& seq, bool contained=false, const std::string& index="") : _id(id), _seq(seq), _contained(contained), _index(index), _color(GC_NONE), _coverage(1) {
  }
  ~Vertex();
 
@@ -121,6 +121,9 @@ class Vertex {
  const std::string& seq() const {
  return _seq;
  }
+ const std::string& index() const {
+ return _index;
+ }
  size_t coverage() const {
  return _coverage;
  }
@@ -173,6 +176,7 @@ class Vertex {
  Id _id;
  GraphColor _color;
  std::string _seq;
+ std::string _index;
  size_t _coverage; // Number of vertices that have been merged into this one
  bool _contained;
 

diff --git a/src/subgraph.cpp b/src/subgraph.cpp
@@ -50,7 +50,7 @@ class SubgraphExtractor {
  void addVertex(const Vertex* vertex, Bigraph* sub) {
  // Make sure the vertex hasn't been added yet
  if (sub->getVertex(vertex->id()) == NULL) {
- sub->addVertex(new Vertex(vertex->id(), vertex->seq(), vertex->contained()));
+ sub->addVertex(new Vertex(vertex->id(), vertex->seq(), vertex->contained(), vertex->index()));
  }
  }