Adding popSTR.cpp as one main binary and others as subcommands.

Author: Snaedis Kristmundsdottir

computePnSlippage.cpp

@@ -573,7 +573,7 @@ void readPnLabels(CharString modelAndLabelDir, CharString iterationNumber, map <
     labelFile.close();
 }
 
-int main(int argc, char const ** argv)
+int main_2(int argc, char const ** argv)
 {
     ComputePnSlippageOptions options;
     ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);

computePnSlippageDefault.cpp

@@ -596,7 +596,7 @@ void readMarkerData(CharString attributesDirectory, Marker marker, map<string, L
     markerToAllelesAndGenotypes[marker].i2 = makeGenotypes(markerToAllelesAndGenotypes[marker].i1);
 }
 
-int main(int argc, char const ** argv)
+int main_3(int argc, char const ** argv)
 {
     ComputePnSlippageOptions options;
     ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);

computeReadAttributes.cpp

@@ -1078,7 +1078,7 @@ Pair<Triple<CharString, CharString, int>,ReadInfo> setReference(BamAlignmentReco
     return returnValue;
 }
 
-int main(int argc, char * argv[])
+int main_1(int argc, char * argv[])
 {
     time_t begin = time(0);
     //Check arguments.

msGenotyper.cpp

@@ -1071,7 +1071,7 @@ long int readOffSets(ifstream & attsFile, unsigned firstPnIdx)
     return offset;
 }
 
-int main(int argc, char const ** argv)
+int main_4(int argc, char const ** argv)
 {
     //Check arguments.
     MsGenotyperOptions options;

msGenotyperDefault.cpp

@@ -1041,7 +1041,7 @@ long int readOffSets(ifstream & attsFile, unsigned firstPnIdx)
     return offset;
 }
 
-int main(int argc, char const ** argv)
+int main_5(int argc, char const ** argv)
 {
     //Check arguments.
     MsGenotyperOptions options;

popSTR.cpp

@@ -0,0 +1,37 @@
+int main_1(int argc, char * argv[]);
+int main_2(int argc, char * argv[]);
+int main_3(int argc, char * argv[]);
+int main_4(int argc, char * argv[]);
+int main_5(int argc, char * argv[]);
+
+int main(int argc, char * argv[])
+{
+	string subcommand = argv[1];
+    if (subcommand == "computeReadAttributes")
+        return main_1(argc-1, argv+1);
+    else
+    {
+    	if (subcommand == "computePnSlippage")
+    		return main_2(argc-1, argv+1);
+    	else
+    	{
+    		if (subcommand == "computePnSlippageDefault")
+    			return main_3(argc-1, argv+1);
+    		else
+    		{
+    			if (subcommand == "msGenotyper")
+    				return main_4(argc-1, argv+1);
+    			else
+    			{
+    				if (subcommand == "msGenotyperDefault")
+    					return main_5(argc-1, argv+1);
+    				else
+    				{
+    					std::cerr << "Unrecognized subcommand, options are: computeReadAttributes, computePnSlippage, computePnSlippageDefault, msGenotyper and msGenotyperDefault.\n";
+    					return 1;
+    				}
+    			}
+    		}
+    	}
+    }
+}