mfa tag desc fix

src/harvest/LcbList.cpp

@@ -39,6 +39,7 @@ void LcbList::initFromMfa(const char * file, ReferenceList * referenceList, Trac
 	vector<string> seqs;
 	const bool oldTags = phylogenyTree->getRoot();
 	string refTag;
+	string refDesc;
 	int * trackIndecesNew;
 
 	if ( oldTags )
@@ -60,12 +61,21 @@ void LcbList::initFromMfa(const char * file, ReferenceList * referenceList, Trac
 		if ( in.peek() == '>' )
 		{
 			in.getline(line, (1 << 20) - 1);
-			string tag(strtok(line + 1, " "));
-			string desc(strtok(0, "\n"));
+			string tag(strtok(line + 1, " \n"));
 
 			if ( seqs.size() == 0 )
 			{
-				refTag = line + 1;
+				const char * desc = strtok(0, "\n");
+
+				if ( desc )
+				{
+					refDesc = desc;
+				}
+			}
+
+			if ( seqs.size() == 0 )
+			{
+				refTag = tag;
 			}
 
 			TrackList::Track * track;
@@ -111,7 +121,7 @@ void LcbList::initFromMfa(const char * file, ReferenceList * referenceList, Trac
 	ungap(ref);
 
 	referenceList->clear();
-	referenceList->addReference(refTag, ref);
+	referenceList->addReference(refTag, refDesc, ref);
 
 	initWithSingleLcb(*referenceList, *trackList);
 
@@ -432,7 +442,7 @@ void LcbList::initFromXmfa(const char * file, ReferenceList * referenceList, Tra
 
 	if ( createReference )
 	{
-		referenceList->addReference(trackList->getTrack(0).file, ref);
+		referenceList->addReference(trackList->getTrack(0).file, "", ref);
 	}
 
 	sort(lcbs.begin(), lcbs.end(), lcbLessThan);

src/harvest/ReferenceList.cpp

@@ -9,10 +9,11 @@
 
 using namespace::std;
 
-void ReferenceList::addReference(string name, string sequence)
+void ReferenceList::addReference(string name, string desc, string sequence)
 {
 	references.resize(references.size() + 1);
 	references[references.size() - 1].name = name;
+	references[references.size() - 1].description = desc;
 	references[references.size() - 1].sequence = sequence;
 }
 

src/harvest/ReferenceList.h

@@ -41,7 +41,7 @@ class ReferenceList
 		std::string gi;
 	};
 
-	void addReference(std::string name, std::string sequence);
+	void addReference(std::string name, std::string desc, std::string sequence);
 	void clear();
 	int getPositionFromConcatenated(int sequence, long int position) const;
 	const Reference & getReference(int index) const;