Scaffolding  0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
File List
Here is a list of all documented files with brief descriptions:
[detail level 12]
  io
 read_adj_list.hpp
 read_dimacs_graph.hpp
 read_dot.hpp
 read_fasta.hpp
 read_phytree.hpp
 scaffold_io.hpp
 write_adj_list.hpp
 write_dimacs_graph.hpp
 write_dot.hpp
 write_fasta.hpp
  preprocess
 jump_preprocess.hpp
 negative_length.hpp
 pp_pendant_match.hpp
 rp_contig_jumps.hpp
  solv
 branching.hpp
 degree_branching.hpp
 dp_solution.hpp
 dp_table.hpp
 FES_branching.hpp
 ilp_common.hpp
 ilp_contig_jumps.hpp
 ilp_model_multi.hpp
 trees.hpp
 tw_dp.hpp
  utils
 adv_edge_iters.hpp
 alternating_path.hpp
 ambigous_paths.hpp
 branching_vector.hpp
 command_line.hpp
 convert.hpp
 exceptions.hpp
 filters.hpp
 graph_infos.hpp
 graph_parameters.hpp
 graph_typedefs.hpp
 graph_utils.hpp
 instance.hpp
 low_priority_queue.hpp
 min_matrix.hpp
 normal_distribution.hpp
 permissive_matching.hpp
 predicates.hpp
 profiling.hpp
 scaffold_graph.hpp
 scaffolding_typedefs.hpp
 scaffolding_utils.hpp
 scoring.hpp
 set_queue.hpp
 solution.hpp
 string_utils.hpp
 td_subgraph.hpp
 unordered_pair.hpp
 utils.hpp