Commit 6aef087f authored by Mathieu Giraud's avatar Mathieu Giraud

core/segment.cpp: use getInfoLine() for .affects debug output (-K)

We thus get evalues.
parent 5b80a9cd
......@@ -149,9 +149,8 @@ bool Segmenter::finishSegmentationD()
string Segmenter::getInfoLine() const
{
string s = ">" ;
string s = "" ;
s += label + " " ;
s += (segmented ? "" : "! ") + info ;
s += " " + info_extra ;
s += " " + segmented_germline->code ;
......@@ -170,6 +169,7 @@ string Segmenter::getInfoLine() const
ostream &operator<<(ostream &out, const Segmenter &s)
{
out << ">" << s.label << " " ;
out << s.getInfoLine() << endl;
if (s.segmented)
......@@ -349,16 +349,17 @@ KmerMultiSegmenter::KmerMultiSegmenter(Sequence seq, MultiGermline *multigermlin
if (out_unsegmented)
{
// Debug, display k-mer affectation and segmentation result for this germline
*out_unsegmented << "#"
<< left << setw(4) << kseg->segmented_germline->code << " "
<< left << setw(20) << segmented_mesg[kseg->getSegmentationStatus()] << " ";
*out_unsegmented << right << setw(3) << kseg->score << " ";
*out_unsegmented << "# "
<< right << setw(3) << kseg->score << " "
<< left << setw(30)
<< kseg->getInfoLine()
<< endl ;
if (kseg->getSegmentationStatus() != UNSEG_TOO_SHORT)
*out_unsegmented << kseg->getKmerAffectAnalyser()->toString();
*out_unsegmented << endl ;
if (kseg->getSegmentationStatus() != UNSEG_TOO_SHORT)
{
*out_unsegmented << kseg->getKmerAffectAnalyser()->toString();
*out_unsegmented << endl ;
}
}
// Always remember the first kseg
......
......@@ -57,7 +57,6 @@ const char* const segmented_mesg[] = { "?",
class Segmenter {
protected:
string label;
string sequence;
int Vend, Jstart;
int Dstart, Dend;
......@@ -71,6 +70,7 @@ protected:
public:
Germline *segmented_germline;
string label;
string code;
string code_short;
string code_light;
......
......@@ -83,7 +83,7 @@ WindowsStorage *WindowExtractor::extract(OnlineFasta *reads, MultiGermline *mult
// Last line of detailed affects output
if (out_affects) {
*out_affects << "#" << seg->getInfoLine() << endl;
*out_affects << "#>" << seg->label << " " << seg->getInfoLine() << endl << endl;
}
// Progress bar
......
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