Commit fb472053 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: default command is '-c clones' (renamed CMD_CLONES)

parent 612230b2
...@@ -75,11 +75,11 @@ ...@@ -75,11 +75,11 @@
#define RATIO_READS_CLONE 0.0 #define RATIO_READS_CLONE 0.0
#define COMMAND_WINDOWS "windows" #define COMMAND_WINDOWS "windows"
#define COMMAND_ANALYSIS "clones" #define COMMAND_CLONES "clones"
#define COMMAND_SEGMENT "segment" #define COMMAND_SEGMENT "segment"
#define COMMAND_GERMLINES "germlines" #define COMMAND_GERMLINES "germlines"
enum { CMD_WINDOWS, CMD_ANALYSIS, CMD_SEGMENT, CMD_GERMLINES } ; enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
#define OUT_DIR "./out/" #define OUT_DIR "./out/"
#define CLONES_FILENAME "clones.vdj.fa" #define CLONES_FILENAME "clones.vdj.fa"
...@@ -135,8 +135,8 @@ void usage(char *progname) ...@@ -135,8 +135,8 @@ void usage(char *progname)
cerr << "Usage: " << progname << " [options] <reads.fa>" << endl << endl; cerr << "Usage: " << progname << " [options] <reads.fa>" << endl << endl;
cerr << "Command selection" << endl cerr << "Command selection" << endl
<< " -c <command> \t" << COMMAND_WINDOWS << "\t window extracting (default)" << endl << " -c <command> \t" << COMMAND_WINDOWS << " \t window extracting" << endl
<< " \t\t" << COMMAND_ANALYSIS << " \t clone analysis" << endl << " \t\t" << COMMAND_CLONES << " \t clone gathering (default)" << endl
<< " \t\t" << COMMAND_SEGMENT << " \t V(D)J segmentation (not recommended)" << endl << " \t\t" << COMMAND_SEGMENT << " \t V(D)J segmentation (not recommended)" << endl
<< " \t\t" << COMMAND_GERMLINES << " \t discover all germlines" << endl << " \t\t" << COMMAND_GERMLINES << " \t discover all germlines" << endl
<< endl << endl
...@@ -210,7 +210,6 @@ void usage(char *progname) ...@@ -210,7 +210,6 @@ void usage(char *progname)
<< endl << endl
<< "Examples (see doc/README)" << endl << "Examples (see doc/README)" << endl
<< " " << progname << " -G germline/IGH -d data/Stanford_S22.fasta" << endl
<< " " << progname << " -c clones -G germline/IGH -r 5 -d data/Stanford_S22.fasta" << endl << " " << progname << " -c clones -G germline/IGH -r 5 -d data/Stanford_S22.fasta" << endl
<< " " << progname << " -c segment -G germline/IGH -d data/Stanford_S22.fasta # (only for testing)" << endl << " " << progname << " -c segment -G germline/IGH -d data/Stanford_S22.fasta # (only for testing)" << endl
<< " " << progname << " -c germlines data/Stanford_S22.fasta" << endl << " " << progname << " -c germlines data/Stanford_S22.fasta" << endl
...@@ -259,7 +258,7 @@ int main (int argc, char **argv) ...@@ -259,7 +258,7 @@ int main (int argc, char **argv)
int segment_D = 0; int segment_D = 0;
int verbose = 0 ; int verbose = 0 ;
int command = CMD_WINDOWS; int command = CMD_CLONES;
int max_clones = MAX_CLONES ; int max_clones = MAX_CLONES ;
int min_reads_clone = MIN_READS_CLONE ; int min_reads_clone = MIN_READS_CLONE ;
...@@ -321,8 +320,8 @@ int main (int argc, char **argv) ...@@ -321,8 +320,8 @@ int main (int argc, char **argv)
detailed_cluster_analysis = false; detailed_cluster_analysis = false;
break; break;
case 'c': case 'c':
if (!strcmp(COMMAND_ANALYSIS,optarg)) if (!strcmp(COMMAND_CLONES,optarg))
command = CMD_ANALYSIS; command = CMD_CLONES;
else if (!strcmp(COMMAND_SEGMENT,optarg)) else if (!strcmp(COMMAND_SEGMENT,optarg))
command = CMD_SEGMENT; command = CMD_SEGMENT;
else if (!strcmp(COMMAND_WINDOWS,optarg)) else if (!strcmp(COMMAND_WINDOWS,optarg))
...@@ -553,7 +552,7 @@ int main (int argc, char **argv) ...@@ -553,7 +552,7 @@ int main (int argc, char **argv)
switch(command) { switch(command) {
case CMD_WINDOWS: cout << "Extracting windows" << endl; case CMD_WINDOWS: cout << "Extracting windows" << endl;
break; break;
case CMD_ANALYSIS: cout << "Analysing clones" << endl; case CMD_CLONES: cout << "Analysing clones" << endl;
break; break;
case CMD_SEGMENT: cout << "Segmenting V(D)J" << endl; case CMD_SEGMENT: cout << "Segmenting V(D)J" << endl;
break; break;
...@@ -763,7 +762,7 @@ int main (int argc, char **argv) ...@@ -763,7 +762,7 @@ int main (int argc, char **argv)
//////////////////////////////////////// ////////////////////////////////////////
// CLONE ANALYSIS // // CLONE ANALYSIS //
//////////////////////////////////////// ////////////////////////////////////////
if (command == CMD_ANALYSIS || command == CMD_WINDOWS) { if (command == CMD_CLONES || command == CMD_WINDOWS) {
////////////////////////////////// //////////////////////////////////
cout << "# seed = " << seed << "," ; cout << "# seed = " << seed << "," ;
...@@ -882,7 +881,7 @@ int main (int argc, char **argv) ...@@ -882,7 +881,7 @@ int main (int argc, char **argv)
list< pair <float, int> > norm_list = compute_normalization_list(windowsStorage->getMap(), normalization, nb_segmented); list< pair <float, int> > norm_list = compute_normalization_list(windowsStorage->getMap(), normalization, nb_segmented);
if (command == CMD_ANALYSIS) { if (command == CMD_CLONES) {
////////////////////////////////// //////////////////////////////////
//$$ min_reads_clone (ou label) //$$ min_reads_clone (ou label)
...@@ -1163,7 +1162,7 @@ int main (int argc, char **argv) ...@@ -1163,7 +1162,7 @@ int main (int argc, char **argv)
} // endif (clones_windows.size() > 0) } // endif (clones_windows.size() > 0)
} // end if (command == CMD_ANALYSIS) } // end if (command == CMD_CLONES)
//$$ .json output: json_data_segment //$$ .json output: json_data_segment
string f_json = out_dir + prefix_filename + "vidjil" + JSON_SUFFIX ; // TODO: retrieve basename from f_reads instead of "vidjil" string f_json = out_dir + prefix_filename + "vidjil" + JSON_SUFFIX ; // TODO: retrieve basename from f_reads instead of "vidjil"
...@@ -1240,7 +1239,7 @@ int main (int argc, char **argv) ...@@ -1240,7 +1239,7 @@ int main (int argc, char **argv)
cout << "* WARNING: vidjil was run with '-c segment' option" << endl cout << "* WARNING: vidjil was run with '-c segment' option" << endl
<< "* Vidjil purpose is to extract very quickly windows overlapping the CDR3" << endl << "* Vidjil purpose is to extract very quickly windows overlapping the CDR3" << endl
<< "* or to gather reads into clones (-c clones), and not to provide an accurate V(D)J segmentation." << endl << "* and to gather reads into clones (-c clones), and not to provide an accurate V(D)J segmentation." << endl
<< "* The following segmentations are slow to compute and are provided only for convenience." << endl << "* The following segmentations are slow to compute and are provided only for convenience." << endl
<< "* They should be checked with other softwares such as IgBlast, iHHMune-align or IMGT/V-QUEST." << endl << "* They should be checked with other softwares such as IgBlast, iHHMune-align or IMGT/V-QUEST." << endl
; ;
......
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