Commit 8b53b47c authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

core/segment.cpp: display segmented germline at the end of fasta header

Useful for '-U' debug output.
parent 610a2390
...@@ -142,6 +142,7 @@ ostream &operator<<(ostream &out, const Segmenter &s) ...@@ -142,6 +142,7 @@ ostream &operator<<(ostream &out, const Segmenter &s)
out << ">" << s.label << " " ; out << ">" << s.label << " " ;
out << (s.segmented ? "" : "! ") << s.info ; out << (s.segmented ? "" : "! ") << s.info ;
out << " " << s.info_extra ; out << " " << s.info_extra ;
out << " " << s.segmented_germline->code ;
out << endl ; out << endl ;
if (s.segmented) if (s.segmented)
...@@ -461,7 +462,7 @@ string format_del(int deletions) ...@@ -461,7 +462,7 @@ string format_del(int deletions)
FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c) FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c)
{ {
segmented_germline = germline ;
info_extra = "" ; info_extra = "" ;
label = seq.label ; label = seq.label ;
sequence = seq.sequence ; sequence = seq.sequence ;
......
...@@ -53,6 +53,7 @@ protected: ...@@ -53,6 +53,7 @@ protected:
bool finishSegmentationD(); bool finishSegmentationD();
public: public:
Germline *segmented_germline;
string code; string code;
string code_short; string code_short;
string code_light; string code_light;
...@@ -140,8 +141,6 @@ class KmerSegmenter : public Segmenter ...@@ -140,8 +141,6 @@ class KmerSegmenter : public Segmenter
string affects; string affects;
public: public:
Germline *segmented_germline;
/** /**
* Build a segmenter based on KmerSegmentation * Build a segmenter based on KmerSegmentation
* @param seq: An object read from a FASTA/FASTQ file * @param seq: An object read from a FASTA/FASTQ file
......
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