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Commit 801c5f8c authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

core/segment.cpp: keeps score of unsegmented sequences, display it in .affects (-u)

parent 8385fe53
......@@ -184,7 +184,9 @@ KmerSegmenter::KmerSegmenter(Sequence seq, Germline *germline)
segmented_germline = germline ;
reversed = false;
Dend=0;
because = 0 ; // Cause of unsegmentation
score = 0 ;
int s = (size_t)germline->index->getS() ;
int length = sequence.length() ;
......@@ -249,11 +251,7 @@ KmerSegmenter::KmerSegmenter(Sequence seq, Germline *germline)
}
}
if (because)
{
score = 0 ;
}
else
if (!because)
{
// Yes, it is segmented
segmented = true;
......@@ -296,10 +294,7 @@ KmerMultiSegmenter::KmerMultiSegmenter(Sequence seq, MultiGermline *multigermlin
<< left << setw(4) << kseg->segmented_germline->code << " "
<< left << setw(20) << segmented_mesg[kseg->getSegmentationStatus()] << " ";
if (kseg->isSegmented())
*out_unsegmented << right << setw(3) << kseg->score << " ";
else
*out_unsegmented << " " ;
*out_unsegmented << right << setw(3) << kseg->score << " ";
if (kseg->getSegmentationStatus() != UNSEG_TOO_SHORT)
*out_unsegmented << kseg->getKmerAffectAnalyser()->toString();
......@@ -336,8 +331,6 @@ void KmerSegmenter::computeSegmentation(int strand, KmerAffect before, KmerAffec
// Try to segment, computing 'Vend' and 'Jstart'
// If not segmented, put the cause of unsegmentation in 'because'
because = 0 ; // Cause of unsegmentation
score = 0 ;
affect_infos max;
max = kaa->getMaximum(before, after);
......
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