Commit 2797ccb0 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: outputs also the representative in 'out/seq/sequences.fa-*'

parent 5abb6395
......@@ -1128,7 +1128,7 @@ int main (int argc, char **argv)
//$$ There is one representative, FineSegmenter
representative.label = string_of_int(it->second) + "-"
representative.label = string_of_int(it->second) + "--"
+ representative.label;
FineSegmenter seg(representative, rep_V, rep_J, delta_min, delta_max, segment_cost);
......@@ -1323,11 +1323,27 @@ int main (int argc, char **argv)
// Output all sequences
Sequence representative
= windowsStorage->getRepresentative(it->first, seed,
min_cover_representative,
ratio_representative,
max_auditionned);
if (representative != NULL_SEQUENCE) {
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)
......@@ -1336,17 +1352,6 @@ int main (int argc, char **argv)
}
}
Sequence representative
= windowsStorage->getRepresentative(it->first, seed,
min_cover_representative,
ratio_representative,
max_auditionned);
if (representative != NULL_SEQUENCE) {
representative.label = string_of_int(it->second) + "-"
+ representative.label;
FineSegmenter seg(representative, rep_V, rep_J, delta_min, delta_max, segment_cost);
if (segment_D)
......
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