Commit 49fa2284 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: remove default germline files

This was source of confusion, in particular in selecting or not D parameters.
Now the code is cleaner.
parent 126b6d15
...@@ -63,10 +63,6 @@ ...@@ -63,10 +63,6 @@
//$$ #define (mainly default options) //$$ #define (mainly default options)
#define DEFAULT_MULTIGERMLINE "germline" #define DEFAULT_MULTIGERMLINE "germline"
#define DEFAULT_GERMLINE_SYSTEM "IGH"
#define DEFAULT_V_REP "./germline/IGHV.fa"
#define DEFAULT_D_REP "./germline/IGHD.fa"
#define DEFAULT_J_REP "./germline/IGHJ.fa"
#define DEFAULT_READS "./data/Stanford_S22.fasta" #define DEFAULT_READS "./data/Stanford_S22.fasta"
#define DEFAULT_MIN_READS_CLONE 5 #define DEFAULT_MIN_READS_CLONE 5
...@@ -147,7 +143,7 @@ void usage(char *progname) ...@@ -147,7 +143,7 @@ void usage(char *progname)
<< " \t\t" << COMMAND_GERMLINES << " \t discover all germlines" << endl << " \t\t" << COMMAND_GERMLINES << " \t discover all germlines" << endl
<< endl << endl
<< "Germline databases" << endl << "Germline databases (one -V/(-D)/-J, or -G, or -g option must be given for all commands except -c " << COMMAND_GERMLINES << ")" << endl
<< " -V <file> V germline multi-fasta file" << endl << " -V <file> V germline multi-fasta file" << endl
<< " -D <file> D germline multi-fasta file (implies -d)" << endl << " -D <file> D germline multi-fasta file (implies -d)" << endl
<< " -J <file> J germline multi-fasta file" << endl << " -J <file> J germline multi-fasta file" << endl
...@@ -237,7 +233,7 @@ int main (int argc, char **argv) ...@@ -237,7 +233,7 @@ int main (int argc, char **argv)
//$$ options: defaults //$$ options: defaults
string germline_system = DEFAULT_GERMLINE_SYSTEM ; string germline_system = "" ;
list <string> f_reps_V ; list <string> f_reps_V ;
list <string> f_reps_D ; list <string> f_reps_D ;
...@@ -346,6 +342,7 @@ int main (int argc, char **argv) ...@@ -346,6 +342,7 @@ int main (int argc, char **argv)
case 'g': case 'g':
multi_germline = true; multi_germline = true;
multi_germline_file = string(optarg); multi_germline_file = string(optarg);
germline_system = "multi" ;
break; break;
case 'G': case 'G':
...@@ -494,6 +491,13 @@ int main (int argc, char **argv) ...@@ -494,6 +491,13 @@ int main (int argc, char **argv)
//$$ options: post-processing+display //$$ options: post-processing+display
if (!germline_system.size() && (command != CMD_GERMLINES))
{
cout << ERROR_STRING << "At least one germline must be given with -V/(-D)/-J, or -G, or -g." << endl ;
exit(1);
}
// If there was no -w option, then w is either DEFAULT_W or DEFAULT_W_D // If there was no -w option, then w is either DEFAULT_W or DEFAULT_W_D
if (w == 0) if (w == 0)
w = default_w ; w = default_w ;
...@@ -526,20 +530,6 @@ int main (int argc, char **argv) ...@@ -526,20 +530,6 @@ int main (int argc, char **argv)
size_t min_cover_representative = (size_t) (min_reads_clone < (int) max_auditionned ? min_reads_clone : max_auditionned) ; size_t min_cover_representative = (size_t) (min_reads_clone < (int) max_auditionned ? min_reads_clone : max_auditionned) ;
// Default repertoires
if (f_reps_V.empty())
f_reps_V.push_back(DEFAULT_V_REP) ;
if (f_reps_D.empty())
f_reps_D.push_back(DEFAULT_D_REP) ;
if (f_reps_J.empty())
f_reps_J.push_back(DEFAULT_J_REP) ;
if (!segment_D)
f_reps_D.clear();
// Default seeds // Default seeds
#ifndef NO_SPACED_SEEDS #ifndef NO_SPACED_SEEDS
......
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