Commit df50db08 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: output_sequences_by_cluster (-a) is done during the first pass

Again, the goal is to remove very_detailed_cluster_analysis.
parent b40adace
......@@ -1116,6 +1116,24 @@ int main (int argc, char **argv)
ratio_representative,
max_auditionned);
representative.label = string_of_int(it->second) + "--" + representative.label;
if (output_sequences_by_cluster) // -a option, output all sequences
{
out_sequences << ">" << it->second << "--window--" << num_seq << " " << windows_labels[it->first] << endl ;
out_sequences << it->first << endl;
if (representative != NULL_SEQUENCE)
out_sequences << representative ;
list<Sequence> &sequences = windowsStorage->getReads(it->first);
for (list<Sequence>::const_iterator itt = sequences.begin(); itt != sequences.end(); ++itt)
{
out_sequences << *itt ;
}
}
if (representative == NULL_SEQUENCE) {
clones_without_representative++ ;
......@@ -1279,10 +1297,8 @@ int main (int argc, char **argv)
num_seq++ ;
string junc = it->first ;
// Output all sequences
Sequence representative
= windowsStorage->getRepresentative(it->first, seed,
min_cover_representative,
......@@ -1294,23 +1310,6 @@ int main (int argc, char **argv)
representative.label = string_of_int(it->second) + "--"
+ representative.label;
if (output_sequences_by_cluster)
{
out_sequences << ">" << it->second << "--window--" << num_seq << " " << windows_labels[it->first] << endl ;
out_sequences << it->first << endl;
if (representative != NULL_SEQUENCE)
out_sequences << representative ;
list<Sequence> &sequences = windowsStorage->getReads(it->first);
for (list<Sequence>::const_iterator itt = sequences.begin(); itt != sequences.end(); ++itt)
{
out_sequences << *itt ;
}
}
representatives_this_clone.push_back(representative);
}
}
......
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