Commit 7e695f73 authored by Mathieu Giraud's avatar Mathieu Giraud

algo/vidjil.cpp: remove 'germline_system', streamline code

This was a relic from ancient times.
parent dcf68c36
......@@ -315,8 +315,6 @@ int main (int argc, char **argv)
//$$ options: defaults
string germline_system = "" ;
list <string> f_reps_V ;
list <string> f_reps_D ;
list <string> f_reps_J ;
......@@ -438,7 +436,6 @@ int main (int argc, char **argv)
case 'V':
f_reps_V.push_back(optarg);
germline_system = "custom" ;
break;
case 'D':
......@@ -448,12 +445,10 @@ int main (int argc, char **argv)
case 'J':
f_reps_J.push_back(optarg);
germline_system = "custom" ;
break;
case 'g':
multi_germline = true;
germline_system = "multi" ;
{
string arg = string(optarg);
struct stat buffer;
......@@ -655,7 +650,7 @@ int main (int argc, char **argv)
//$$ options: post-processing+display
if (!germline_system.size())
if (!multi_germline && (!f_reps_V.size() || !f_reps_J.size()))
{
cerr << ERROR_STRING << "At least one germline must be given with -g or -V/(-D)/-J." << endl ;
exit(1);
......@@ -693,15 +688,7 @@ int main (int argc, char **argv)
#ifndef NO_SPACED_SEEDS
if (kmer_size == DEFAULT_K)
{
if (germline_system.find("TRA") != string::npos)
seed = SEED_S13 ;
else if ((germline_system.find("TRB") != string::npos)
|| (germline_system.find("IGH") != string::npos))
seed = SEED_S12 ;
else // TRD, TRG, IGK, IGL, custom, multi
seed = SEED_S10 ;
seed = SEED_S10 ;
kmer_size = seed_weight(seed);
}
#else
......@@ -861,7 +848,7 @@ int main (int argc, char **argv)
{
// Custom germline
Germline *germline;
germline = new Germline(germline_system, 'X',
germline = new Germline("custom", 'X',
f_reps_V, f_reps_D, f_reps_J,
delta_min, seed, trim_sequences);
......
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