Commit 9426c9a9 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: use SampleOutputAIRR(), output .tsv AIRR

See #2828.
parent 83e65abd
...@@ -103,6 +103,7 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ; ...@@ -103,6 +103,7 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
#define AFFECTS_FILENAME ".affects" #define AFFECTS_FILENAME ".affects"
#define EDGES_FILENAME ".edges" #define EDGES_FILENAME ".edges"
#define COMP_FILENAME "comp.vidjil" #define COMP_FILENAME "comp.vidjil"
#define AIRR_SUFFIX ".tsv"
#define JSON_SUFFIX ".vidjil" #define JSON_SUFFIX ".vidjil"
#define DEFAULT_K 0 #define DEFAULT_K 0
...@@ -753,6 +754,7 @@ int main (int argc, char **argv) ...@@ -753,6 +754,7 @@ int main (int argc, char **argv)
// JSON OUTPUT // // JSON OUTPUT //
///////////////////////////////////////// /////////////////////////////////////////
string f_airr = out_dir + f_basename + AIRR_SUFFIX ;
string f_json = out_dir + f_basename + JSON_SUFFIX ; string f_json = out_dir + f_basename + JSON_SUFFIX ;
ostringstream stream_cmdline; ostringstream stream_cmdline;
...@@ -1638,13 +1640,19 @@ int main (int argc, char **argv) ...@@ -1638,13 +1640,19 @@ int main (int argc, char **argv)
cout << endl; cout << endl;
} }
//$ Output AIRR .tsv
cout << " ==> " << f_airr << " \t(AIRR output)" << endl;
ofstream out_airr(f_airr.c_str());
static_cast<SampleOutputAIRR *>(output) -> out(out_airr);
//$ Output .vidjil json //$ Output .vidjil json
cout << " ==> " << f_json << "\t(data file for the web application)" << endl ; cout << " ==> " << f_json << "\t(data file for the Vidjil web application)" << endl ;
ofstream out_json(f_json.c_str()) ; ofstream out_json(f_json.c_str()) ;
SampleOutputVidjil *outputVidjil = static_cast<SampleOutputVidjil *>(output); SampleOutputVidjil *outputVidjil = static_cast<SampleOutputVidjil *>(output);
outputVidjil->out(out_json); outputVidjil->out(out_json);
//$$ Clean //$$ Clean
delete multigermline ; delete multigermline ;
delete reads; delete reads;
......
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