Commit 2bead3c9 authored by Mathieu Giraud's avatar Mathieu Giraud

core/segment.{h,cpp}: JUNCTION output on stdout

Clean stdout. We just report here the JUNCTION, including Cys104 and Phe118/Trp118.
parent e26acaaa
......@@ -255,8 +255,8 @@ string Segmenter::getInfoLine() const
s += "/" + scientific_string_of_double(evalue_right);
if (CDR3start > 0)
s += " {CDR3: " + string_of_int(CDR3start) + "(" + string_of_int(CDR3end-CDR3start+1) + ")" + string_of_int(CDR3end) + " "
+ "up"[CDR3productive] + " " + JUNCTIONaa + " " + CDR3nuc + "}";
s += " {" + string_of_int(JUNCTIONstart) + "(" + string_of_int(JUNCTIONend-JUNCTIONstart+1) + ")" + string_of_int(JUNCTIONend) + " "
+ "up"[JUNCTIONproductive] + " " + JUNCTIONaa + "}";
return s ;
}
......@@ -1074,7 +1074,7 @@ void FineSegmenter::findCDR3(){
JUNCTIONaa = nuc_to_aa(subsequence(getSequence().sequence, JUNCTIONstart, CDR3start-1))
+ CDR3aa + nuc_to_aa(subsequence(getSequence().sequence, CDR3end+1, JUNCTIONend));
CDR3productive = (CDR3nuc.length() % 3 == 0) && (CDR3aa.find('*') == string::npos);
JUNCTIONproductive = (CDR3nuc.length() % 3 == 0) && (JUNCTIONaa.find('*') == string::npos);
}
json FineSegmenter::toJson(){
......@@ -1099,13 +1099,13 @@ json FineSegmenter::toJson(){
seg["cdr3"] = {
{"start", CDR3start},
{"stop", CDR3end},
{"aa", CDR3aa},
{"productive", CDR3productive}
{"aa", CDR3aa}
};
seg["junction"] = {
{"start", JUNCTIONstart},
{"stop", JUNCTIONend},
{"aa", JUNCTIONaa}
{"aa", JUNCTIONaa},
{"productive", JUNCTIONproductive}
};
}
}
......
......@@ -125,11 +125,11 @@ protected:
int JUNCTIONstart, JUNCTIONend;
string JUNCTIONaa;
bool JUNCTIONproductive;
int CDR3start, CDR3end;
string CDR3nuc;
string CDR3aa;
bool CDR3productive;
bool reversed, segmented, dSegmented;
int because;
......
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