Commit d10ee62d authored by Mathieu Giraud's avatar Mathieu Giraud

core/segment.cpp: light refactoring of FineSegmenter unsegmentation causes

No functional modifications.
parent 7e632481
......@@ -731,33 +731,33 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c)
score_J=score_minus_J;
}
segmented = (Vend != (int) string::npos) && (Jstart != (int) string::npos) &&
(Jstart - Vend >= germline->delta_min);
if (!segmented)
/* Unsegmentation causes */
if (Jstart - Vend < germline->delta_min)
{
because = NOT_PROCESSED;
info = " @" + string_of_int (Vend + FIRST_POS) + " @" + string_of_int(Jstart + FIRST_POS) ;
if (Jstart - Vend < germline->delta_min)
{
because = UNSEG_BAD_DELTA_MIN ;
}
because = UNSEG_BAD_DELTA_MIN ;
}
if (Vend == (int) string::npos)
{
because = UNSEG_TOO_FEW_V ;
}
if (Jstart == (int) string::npos)
{
because = UNSEG_TOO_FEW_J ;
}
if (Vend == (int) string::npos)
{
because = UNSEG_TOO_FEW_V ;
}
if (Jstart == (int) string::npos)
{
because = UNSEG_TOO_FEW_J ;
}
if (because != NOT_PROCESSED)
{
segmented = false;
info = " @" + string_of_int (Vend + FIRST_POS) + " @" + string_of_int(Jstart + FIRST_POS) ;
return ;
}
because = reversed ? SEG_MINUS : SEG_PLUS ;
/* The sequence is segmented */
segmented = true ;
because = reversed ? SEG_MINUS : SEG_PLUS ;
//overlap VJ
if(Jstart-Vend <=0){
......
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