예제 #1
0
//TODO: translate this
void haplo_d::initialize_skeleton(thread_t& t, pair<int,int> interval, cross_section& prevAs, xg::XG& graph) {
  rectangle rect;
  int new_height;
  int last_height = prevAs.S[0].J;
  bool add_rectangle;
  bool add_A;
  //TODO: fix this
  int width = 0;
  for(int i = interval.first; i <= interval.second; i++) {
    // Count the number of base pairs since the last entry or exit node
    width += graph.node_length(t[i-1].node_id);
    new_height = graph.node_height(t[i]);
    if(cs.back().S.size() != 0) {
      if(i == interval.first) {
        prevAs.S[0];
      } else {
        rect = cs.back().S[0];
      }
      rect.J = rect.get_next_J(t[i],graph); // step this strip forward
      // Did any threads leave?
      if(last_height > rect.J) {
        add_A = 1;
      }
      // Are there any threads here which didn't come from the previous node?
      if(rect.J < new_height) {
        add_rectangle = 1;
        add_A = 1;
      }
      // This is an entry or exit node, add a cross-section to the vector of
      // cross-sections (which corresponds to the "A" set in the theory doc)
      if(add_A) {
        cs.back().width = width;
        width = 0;
        cs.push_back(cross_section(new_height,i,t[i]));
      } else {
        // This isn't a node where anything leaves or joins, let's skip over it
        cs.back().bridge.push_back(t[i]);
        for (size_t a = 0; a < cs.back().S.size(); a++) {
          cs.back().S[a].extend(t[i],graph);
        }
      }
      // This is an entry node; we also need a new rectangle corresponding to the
      // new strip. We need to do this *before* we populate since cross_sections
      // arrange rectangles newest -> oldest
      // NB that add_rectangle implies add_A
      if(add_rectangle) {
        rectangle new_rect;
        new_rect.extend(t[i],graph);
        new_rect.J = new_height;
        cs.back().height = new_rect.J;
        cs.back().S.push_back(new_rect);
        cs.back().S.back().I = new_rect.J - rect.J;
      }
      if(add_A) {
        int b = cs.size()-1;
        if(rect.J > 0) {
          cs[b].S.push_back(rect);
          cs[b].S.back().prev = 0;
          cs[b-1].S[0].next = cs[b].S.size()-1;
        }
      }
      last_height = new_height;
      add_A = 0;
      add_rectangle = 0;
    } else {
      cs.back().width = width;
      width = 0;
      cs.push_back(cross_section(new_height,i,t[i]));
      if(new_height > 0) {
        rectangle new_rect;
        new_rect.extend(t[i],graph);
        new_rect.J = new_height;
        cs.back().height = new_rect.J;
        cs.back().S.push_back(new_rect);
        cs.back().S.back().I = new_rect.J - rect.J;
      }
    }
  }
  if(cs.size() == 1) {
    cs.back().width = width;
  }
  cs.back().width += graph.node_length(t.back().node_id) - 1;
  for(int i = 0; i < cs.size(); i++) {
    tot_width += cs[i].width;
  }
}
예제 #2
0
파일: path_index.cpp 프로젝트: cmarkello/vg
PathIndex::PathIndex(const Path& path, const xg::XG& index) {
    // Trace the given path in the given XG graph, collecting sequence
    
    // We're going to build the sequence string
    std::stringstream seq_stream;
    
    // What base are we at in the path?
    size_t path_base = 0;
    
    // What was the last rank? Ranks must always go up.
    int64_t last_rank = -1;
    
    for (size_t i = 0; i < path.mapping_size(); i++) {
        auto& mapping = path.mapping(i);
    
        if (!by_id.count(mapping.position().node_id())) {
            // This is the first time we have visited this node in the path.
            
            // Add in a mapping.
            by_id[mapping.position().node_id()] = 
                std::make_pair(path_base, mapping.position().is_reverse());
#ifdef debug
            #pragma omp critical (cerr)
            std::cerr << "Node " << mapping.position().node_id() << " rank " << mapping.rank()
                << " starts at base " << path_base << " with "
                << index.node_sequence(mapping.position().node_id()) << std::endl;
#endif
            
            // Make sure ranks are monotonically increasing along the path, or
            // unset.
            assert(mapping.rank() > last_rank || (mapping.rank() == 0 && last_rank == 0));
            last_rank = mapping.rank();
        }
        
        // Say that this node appears here along the reference in this
        // orientation.
        by_start[path_base] = NodeSide(mapping.position().node_id(), mapping.position().is_reverse());
    
        // Remember that occurrence by node ID.
        node_occurrences[mapping.position().node_id()].push_back(by_start.find(path_base));
    
        // Find the node's sequence
        std::string node_sequence = index.node_sequence(mapping.position().node_id());
    
        while(path_base == 0 && node_sequence.size() > 0 &&
            (node_sequence[0] != 'A' && node_sequence[0] != 'T' && node_sequence[0] != 'C' &&
            node_sequence[0] != 'G' && node_sequence[0] != 'N')) {
            
            // If the path leads with invalid characters (like "X"), throw them
            // out when computing path positions.
            
            // TODO: this is a hack to deal with the debruijn-brca1-k63 graph,
            // which leads with an X.
            #pragma omp critical (cerr)
            std::cerr << "Warning: dropping invalid leading character "
                << node_sequence[0] << " from node " << mapping.position().node_id()
                << std::endl;
                
            node_sequence.erase(node_sequence.begin());
        }
        
        if (mapping.position().is_reverse()) {
            // Put the reverse sequence in the path
            seq_stream << reverse_complement(node_sequence);
        } else {
            // Put the forward sequence in the path
            seq_stream << node_sequence;
        }
        
        // Whether we found the right place for this node in the reference or
        // not, we still need to advance along the reference path. We assume the
        // whole node (except any leading bogus characters) is included in the
        // path (since it sort of has to be, syntactically, unless it's the
        // first or last node).
        path_base += node_sequence.size();
        
        // TODO: handle leading bogus characters in calls on the first node.
    }
    
    // Record the length of the last mapping's node, since there's no next mapping to work it out from
    last_node_length = path.mapping_size() > 0 ?
        index.node_length(path.mapping(path.mapping_size() - 1).position().node_id()) :
        0;
    
    // Create the actual reference sequence we will use
    sequence = seq_stream.str();
    
#ifdef debug
    // Announce progress.
    #pragma omp critical (cerr)
    std::cerr << "Traced " << path_base << " bp path." << std::endl;
    
    if (sequence.size() < 100) {
        #pragma omp critical (cerr)
        std::cerr << "Sequence: " << sequence << std::endl;
    }
#endif

}