Scaffolding  0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
Functions | Variables
command_line.hpp File Reference
#include <string>
#include <boost/program_options/variables_map.hpp>
#include <boost/program_options/parsers.hpp>
#include "utils/utils.hpp"
#include "utils/exceptions.hpp"

Go to the source code of this file.

Functions

template<typename T >
const T & get_option (const po::variables_map &vm, const std::string &option_name, const T &default_value)
 return the value of an option or the given default if the value has not been supplied
 
void handle_options (const int argc, const char **argv)
 process the program options given on the command line
 

Variables

struct {
   std::string   in_graph_filename
 filename of the input graph
 
   std::string   in_seq_filename
 filename of the input sequence file in fasta format
 
   std::string   out_model_filename
 filename of a file to export the cplex model to
 
   std::string   out_graph_filename
 filename of a file to export the solution graph to
 
   std::string   out_seq_filename
 filename of a file to export solution sequences to
 
   bool   preprocess
 bool indicating whether to run preprocessing or not (currently defunct)
 
   bool   multi_take_all
 bool indicating whether taking a contig-connection with multiplicity will gain all its weight More...
 
   bool   ignore_contig_jumps
 bool incidating whether contig jumps should be considered More...
 
   unsigned   objects
 maximum number of objects (paths or cycles) that a solution graph should consist of
 
   unsigned   paths
 maximum number of paths that a solution graph should consist of
 
   unsigned   cycles
 maximum number of cycles that a solution graph should consist of
 
   unsigned   cut_off
 cut-off threshold: remove all links between contigs whose weight is strictly below this threshold
 
options
 options that configure the scaffolder
 

Detailed Description

command-line interface handling parameters and options

Variable Documentation

bool ignore_contig_jumps

bool incidating whether contig jumps should be considered

A contig jump is a read-pair whose ends are in contigs A & C, but in the genome there is a contig B between them

bool multi_take_all

bool indicating whether taking a contig-connection with multiplicity will gain all its weight

if true, its weight will be gained if it is being used, no matter how often if false, each time it is being taken, we gain a portion of its weight up to its full weight at its maximum multiplicity