vidjil.cpp: '-a' option also sets very_detailed_analysis

To actually output 'out/seq/sequences.fa-*', we need to run this somewhat old code

algo/vidjil.cpp

@@ -205,7 +205,7 @@ void usage(char *progname)
        << "  -o <dir>      output directory (default: " << OUT_DIR << ")" <<  endl
        << "  -p <string>   prefix output filenames by the specified string" << endl
     
-       << "  -a            output all sequences by cluster (" << SEQUENCES_FILENAME << ")" << endl
+       << "  -a            output all sequences by cluster (" << SEQUENCES_FILENAME << "), to be used only on small datasets" << endl
        << "  -x            do not compute representative sequences" << endl
        << "  -v            verbose mode" << endl
        << endl        
@@ -307,6 +307,7 @@ int main (int argc, char **argv)
         usage(argv[0]);
       case 'a':
 	output_sequences_by_cluster = true;
+	very_detailed_cluster_analysis = true;
 	break;
       case 'd':
 	segment_D = 1 ;

doc/algo.org

@@ -69,8 +69,7 @@ make test                # run self-tests
 These dependencies have no consequences on the visualization through the
 browser. They are intented for a command-line use only.
 
-- clustalw :: to compute alignments between windows from a same clone, by setting 
-          =very_detailed_cluster_analysis= in vidjil.cpp
+- clustalw :: to compute alignments between windows from a same clone (with =-a= option)
 - neato :: to display graph of neighbors for the automatic clusterisation
 
 * Vidjil parameters