Update to print any-to-any migration rates in mig skyline.

Author: trvrb

coaltree.cpp

@@ -297,6 +297,12 @@ CoalescentTree::CoalescentTree(string paren) {
 					(*it).setX(xloc);				
 				}	
 
+				// iSNV
+				if (stringOne == "iSNV") {
+					double xloc = atof(stringTwo.c_str());
+					(*it).setX(xloc);				
+				}					
+				
 				// LATITUDE
 				if (stringOne == "latitude") {
 					double xloc = atof(stringTwo.c_str());

io.cpp

@@ -844,6 +844,20 @@ void IO::printSkylines() {
 		// MIGRATION ///////////////////////
 		if (param.skyline_mig_rates) {		
 			cout << "Printing migration skyline to " << outputFile << endl;
+			
+			for (double t = start; t + step <= stop; t += step) {
+				Series s;
+				for (int i = 0; i < treelist.size(); i++) {
+					CoalescentTree ct = treelist[i];
+					ct.trimEnds(t,t+step);				
+					double n = ct.getMigRate();
+					s.insert(n);
+				}
+				outStream << "mig_all\t";
+				outStream << t + step / (double) 2 << "\t";
+				outStream << s.quantile(0.025) << "\t" << s.mean() << "\t" << s.quantile(0.975) << endl;
+			}
+			
 			for (is = lset.begin(); is != lset.end(); ++is) {
 				for (js = lset.begin(); js != lset.end(); ++js) {	
 					string from = *is;

param.cpp

@@ -146,7 +146,7 @@ void Parameters::importLine(string line) {
 			break; 
 		else if (*is >= 'a' && *is <= 'z' && vstring.size() == 0)
     		pstring += *is;
-		else if ( (*is >= '0' && *is <= '9') || (*is >= 'a' && *is <= 'z') || (*is >= 'A' && *is <= 'Z') || *is == '.' || *is == '-' || *is == '/' || *is == '_')
+		else if ( (*is >= '0' && *is <= '9') || (*is >= 'a' && *is <= 'z') || (*is >= 'A' && *is <= 'Z') || *is == '.' || *is == '-' || *is == '/' || *is == '_' || *is == '|')
     		vstring += *is;
     	else if (vstring.size() > 0) {
     		values.push_back( atof(vstring.c_str()) );