Commit c1ac9fac authored by Mathieu Giraud's avatar Mathieu Giraud

core/segment.cpp, core/kmerstore.h: MAX1U, report information through FineSegmenter

parent 8ea42fff
...@@ -333,7 +333,7 @@ string IKmerStore<T>::getLabel(T kmer) const { ...@@ -333,7 +333,7 @@ string IKmerStore<T>::getLabel(T kmer) const {
for (typename list< pair<T, string> >::const_iterator it = labels.begin(); it != labels.end(); ++it) for (typename list< pair<T, string> >::const_iterator it = labels.begin(); it != labels.end(); ++it)
if (it->first == kmer) if (it->first == kmer)
return it->second ; return it->second ;
return "" ; return "?" ;
} }
// .getResults() // .getResults()
......
...@@ -642,9 +642,10 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c) ...@@ -642,9 +642,10 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c)
if (!germline->rep_5.size() || !germline->rep_3.size()) if (!germline->rep_5.size() || !germline->rep_3.size())
{ {
// We check whether this sequence is segmented with MAX12 (with default e-value parameters) // We check whether this sequence is segmented with MAX12 or MAX1U (with default e-value parameters)
KmerSegmenter *kseg = new KmerSegmenter(seq, germline, THRESHOLD_NB_EXPECTED, 1); KmerSegmenter *kseg = new KmerSegmenter(seq, germline, THRESHOLD_NB_EXPECTED, 1);
if (kseg->isSegmented() && (!strcmp(germline->code.c_str(), PSEUDO_GERMLINE_MAX12))) if (kseg->isSegmented() && ((!strcmp(germline->code.c_str(), PSEUDO_GERMLINE_MAX12))
|| !strcmp(germline->code.c_str(), PSEUDO_GERMLINE_MAX1U)))
{ {
reversed = kseg->isReverse(); reversed = kseg->isReverse();
......
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