Commit 2c253575 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: bikeshedding, streamline DEFAULT_ macro names

parent e003700b
......@@ -69,10 +69,10 @@
#define DEFAULT_J_REP "./germline/IGHJ.fa"
#define DEFAULT_READS "./data/Stanford_S22.fasta"
#define MIN_READS_CLONE 5
#define DEFAULT_MIN_READS_CLONE 5
#define DEFAULT_MAX_REPRESENTATIVES 100
#define MAX_CLONES 20
#define RATIO_READS_CLONE 0.0
#define DEFAULT_MAX_CLONES 20
#define DEFAULT_RATIO_READS_CLONE 0.0
#define NO_LIMIT "all"
#define COMMAND_WINDOWS "windows"
......@@ -82,7 +82,9 @@
enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
#define OUT_DIR "./out/"
#define DEFAULT_OUT_DIR "./out/"
// Fixed filenames/suffixes
#define CLONES_FILENAME ".vdj.fa"
#define CLONE_FILENAME "clone.fa-"
#define WINDOWS_FILENAME ".windows.fa"
......@@ -121,7 +123,7 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
// display
#define WIDTH_NB_READS 7
#define WIDTH_NB_CLONES 3
#define WIDTH_WINDOW_POS 14+WIDTH_NB_CLONES
using namespace std ;
......@@ -170,13 +172,13 @@ void usage(char *progname)
<< endl
<< "Limits to report a clone (or a window)" << endl
<< " -r <nb> minimal number of reads supporting a clone (default: " << MIN_READS_CLONE << ")" << endl
<< " -% <ratio> minimal percentage of reads supporting a clone (default: " << RATIO_READS_CLONE << ")" << endl
<< " -r <nb> minimal number of reads supporting a clone (default: " << DEFAULT_MIN_READS_CLONE << ")" << endl
<< " -% <ratio> minimal percentage of reads supporting a clone (default: " << DEFAULT_RATIO_READS_CLONE << ")" << endl
<< endl
<< "Limits to further analyze some clones" << endl
<< " -y <nb> maximal number of clones computed with a representative ('" << NO_LIMIT << "': no limit) (default: " << DEFAULT_MAX_REPRESENTATIVES << ")" << endl
<< " -z <nb> maximal number of clones to be segmented ('" << NO_LIMIT << "': no limit, do not use) (default: " << MAX_CLONES << ")" << endl
<< " -z <nb> maximal number of clones to be segmented ('" << NO_LIMIT << "': no limit, do not use) (default: " << DEFAULT_MAX_CLONES << ")" << endl
<< " -A reports and segments all clones (-r 0 -% 0 -y " << NO_LIMIT << " -z " << NO_LIMIT << "), to be used only on very small datasets" << endl
<< endl
......@@ -199,7 +201,7 @@ void usage(char *progname)
<< " -u output unsegmented (in " << UNSEGMENTED_FILENAME << " file) sequences" << endl
<< " and display detailed k-mer affectation both on segmented and on unsegmented sequences" << endl
<< "Output" << endl
<< " -o <dir> output directory (default: " << OUT_DIR << ")" << endl
<< " -o <dir> output directory (default: " << DEFAULT_OUT_DIR << ")" << endl
<< " -b <string> output basename (by default basename of the input file)" << endl
<< " -a output all sequences by cluster (" << CLONE_FILENAME << "*), to be used only on small datasets" << endl
......@@ -242,7 +244,7 @@ int main (int argc, char **argv)
string seed = DEFAULT_SEED ;
string f_basename = "";
string out_dir = OUT_DIR;
string out_dir = DEFAULT_OUT_DIR;
string comp_filename = COMP_FILENAME;
......@@ -264,9 +266,9 @@ int main (int argc, char **argv)
int command = CMD_CLONES;
int max_representatives = DEFAULT_MAX_REPRESENTATIVES ;
int max_clones = MAX_CLONES ;
int min_reads_clone = MIN_READS_CLONE ;
float ratio_reads_clone = RATIO_READS_CLONE;
int max_clones = DEFAULT_MAX_CLONES ;
int min_reads_clone = DEFAULT_MIN_READS_CLONE ;
float ratio_reads_clone = DEFAULT_RATIO_READS_CLONE;
// int average_deletion = 4; // Average number of deletion in V or J
float ratio_representative = DEFAULT_RATIO_REPRESENTATIVE;
......
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