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Commit be1c678e authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

algo/vidjil.cpp: '-c segment' also uses KmerMultiSegmenter

Now the best germline is selected (by KmerSegmenter) to launch the FineSegmenter.
It gives a better output for '-c segment' with multi-germlines.
parent 13380ba7
......@@ -717,9 +717,7 @@ int main (int argc, char **argv)
f_reps_V, f_reps_D, f_reps_J,
delta_min, delta_max);
if (command == CMD_WINDOWS || command == CMD_CLONES)
germline->new_index(seed);
germline->new_index(seed);
multigermline->insert(germline);
}
......@@ -1359,12 +1357,10 @@ int main (int argc, char **argv)
reads->next();
Sequence seq = reads->getSequence() ;
bool segmented = false ;
for (list<Germline*>::const_iterator it = multigermline->germlines.begin(); it != multigermline->germlines.end(); ++it)
{
Germline *germline = *it ;
KmerMultiSegmenter kmseg(reads->getSequence(), multigermline, NULL); // out_unsegmented);
KmerSegmenter *seg = kmseg.the_kseg ;
Germline *germline = seg->segmented_germline ;
FineSegmenter s(seq, germline, segment_cost);
if (s.isSegmented())
......@@ -1374,22 +1370,9 @@ int main (int argc, char **argv)
if (detect_CDR3)
s.findCDR3();
cout << s << endl;
segmented = true ;
break ;
}
else
{
if (verbose)
cout << "# " << germline->code << ": unable to segment" << endl;
}
}
if (!segmented)
{
seq.label += " unsegmented";
cout << seq << endl;
}
cout << s << endl;
}
} else {
......
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