Commit 5abb6395 authored by Mathieu Giraud's avatar Mathieu Giraud

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

To actually output 'out/seq/sequences.fa-*', we need to run this somewhat old code
parent cafd79c1
......@@ -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 ;
......
......@@ -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
......
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