Commit 444055e9 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: reports in 'out/clones.vdj.fa' all windows, even without representative/segmentation

parent b08a0c04
......@@ -999,14 +999,6 @@ int main (int argc, char **argv)
++num_clone ;
if (max_clones && (num_clone == max_clones + 1))
break ;
cout << "#### " ;
string clone_file_name = out_seqdir+ prefix_filename + CLONE_FILENAME + string_of_int(num_clone) ;
ofstream out_clone(clone_file_name.c_str());
Germline *segmented_germline = windowsStorage->getGermline(it->first);
//$$ Computing labels
......@@ -1028,12 +1020,29 @@ int main (int argc, char **argv)
<< " – " << 100 * (float) clone_nb_reads * compute_normalization_one(norm_list, clone_nb_reads) / nb_segmented << "% "
<< compute_normalization_one(norm_list, clone_nb_reads) << " " ;
string clone_id_human = oss_human.str();
// Window label
string window_str = ">" + clone_id + "--window" + " " + windows_labels[it->first] + '\n' + it->first + '\n' ;
//$$ If max_clones is reached, we stop here but still outputs the window
if (max_clones && (num_clone >= max_clones + 1))
{
out_clones << window_str << endl ;
continue;
}
cout << clone_id_human << endl ;
//$$ Open CLONE_FILENAME
//$$ Output window
string clone_file_name = out_seqdir+ prefix_filename + CLONE_FILENAME + string_of_int(num_clone) ;
ofstream out_clone(clone_file_name.c_str());
string window_str = ">" + clone_id + "--window" + " " + windows_labels[it->first] + '\n' + it->first + '\n' ;;
//$$ Output window
cout << window_str ;
out_clone << window_str ;
......
Markdown is supported
0%
or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment