Scaffolding
0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
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#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 | |
command-line interface handling parameters and options
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