Commit b59a820d authored by Mikaël Salson's avatar Mikaël Salson
Browse files

vidjil.cpp: Use new version of index creation.

Makes it ready to support a parameter to choose the index.
parent 167a3575
...@@ -331,6 +331,8 @@ int main (int argc, char **argv) ...@@ -331,6 +331,8 @@ int main (int argc, char **argv)
int k = DEFAULT_K ; int k = DEFAULT_K ;
int w = DEFAULT_W ; int w = DEFAULT_W ;
IndexTypes indexType = AC_AUTOMATON;
int epsilon = DEFAULT_EPSILON ; int epsilon = DEFAULT_EPSILON ;
int minPts = DEFAULT_MINPTS ; int minPts = DEFAULT_MINPTS ;
Cost cluster_cost = DEFAULT_CLUSTER_COST ; Cost cluster_cost = DEFAULT_CLUSTER_COST ;
...@@ -860,7 +862,7 @@ int main (int argc, char **argv) ...@@ -860,7 +862,7 @@ int main (int argc, char **argv)
multi_germline_paths_and_files.push_back(make_pair(DEFAULT_MULTI_GERMLINE_PATH, DEFAULT_MULTI_GERMLINE_FILE)); multi_germline_paths_and_files.push_back(make_pair(DEFAULT_MULTI_GERMLINE_PATH, DEFAULT_MULTI_GERMLINE_FILE));
} }
MultiGermline *multigermline = new MultiGermline(multi_germline_one_index_per_germline); MultiGermline *multigermline = new MultiGermline(indexType, multi_germline_one_index_per_germline);
{ {
cout << "Load germlines and build Kmer indexes" << endl ; cout << "Load germlines and build Kmer indexes" << endl ;
...@@ -878,7 +880,7 @@ int main (int argc, char **argv) ...@@ -878,7 +880,7 @@ int main (int argc, char **argv)
f_reps_V, f_reps_D, f_reps_J, f_reps_V, f_reps_D, f_reps_J,
delta_min, seed, trim_sequences); delta_min, seed, trim_sequences);
germline->new_index(); germline->new_index(indexType);
multigermline->insert(germline); multigermline->insert(germline);
} }
......
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