Commit 2d80348c authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: default window is now 50, both for VJ and V(D)J recombinations

Previously, the default -w was 40 for VJ, and 60 for V(D)J, except in
multi-locus identification (-g), when it was 40 even for V(D)J recombinations.
For the majority of cases, setting -w to 50 is thus more conservative.
Many users already tested -w 50 (or the less conservative -w 40) for IGH and
found correct results.

Now we have a uniform window size for all locus, allowing a better indexing
and comparison of windows across experiments and configurations.
parent b5266f80
......@@ -98,8 +98,7 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
// "tests/data/leukemia.fa"
#define DEFAULT_K 0
#define DEFAULT_W 40
#define DEFAULT_W_D 60
#define DEFAULT_W 50
#define DEFAULT_SEED ""
#define DEFAULT_DELTA_MIN -10
......@@ -179,7 +178,7 @@ void usage(char *progname, bool advanced)
#endif
<< " -m <int> minimal admissible delta between last V and first J k-mer (default: " << DEFAULT_DELTA_MIN << ") (default with -D: " << DEFAULT_DELTA_MIN_D << ")" << endl
<< " -M <int> maximal admissible delta between last V and first J k-mer (default: " << DEFAULT_DELTA_MAX << ") (default with -D: " << DEFAULT_DELTA_MAX_D << ")" << endl
<< " -w <int> w-mer size used for the length of the extracted window (default: " << DEFAULT_W << ") (default with -D: " << DEFAULT_W_D << ")" << endl
<< " -w <int> w-mer size used for the length of the extracted window (default: " << DEFAULT_W << ")" << endl
<< " -e <float> maximal e-value for determining if a segmentation can be trusted (default: " << THRESHOLD_NB_EXPECTED << ")" << endl
<< endl
......@@ -286,8 +285,7 @@ int main (int argc, char **argv)
string comp_filename = COMP_FILENAME;
int k = DEFAULT_K ;
int w = 0 ;
int default_w = DEFAULT_W ;
int w = DEFAULT_W ;
int epsilon = DEFAULT_EPSILON ;
int minPts = DEFAULT_MINPTS ;
......@@ -383,7 +381,6 @@ int main (int argc, char **argv)
f_reps_D.push_back(optarg);
delta_min = DEFAULT_DELTA_MIN_D ;
delta_max = DEFAULT_DELTA_MAX_D ;
default_w = DEFAULT_W_D ;
break;
case 'J':
......@@ -425,7 +422,6 @@ int main (int argc, char **argv)
f_reps_D.push_back(putative_f_rep_D.c_str()) ;
delta_min = DEFAULT_DELTA_MIN_D ;
delta_max = DEFAULT_DELTA_MAX_D ;
default_w = DEFAULT_W_D ;
}
}
f_reps_J.push_back((germline_system + "J.fa").c_str()) ;
......@@ -582,11 +578,6 @@ int main (int argc, char **argv)
exit(1);
}
// If there was no -w option, then w is either DEFAULT_W or DEFAULT_W_D
if (w == 0)
w = default_w ;
if (options_s_k > 1)
{
cerr << ERROR_STRING << "Use at most one -s or -k option." << endl ;
......
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