Fixed "pure virtual method called" error, and "dereferencing type-pun…

…ned pointer" warning

Makefile

@@ -34,6 +34,8 @@ INSTALLLIB=/software/varinf/lib
 INSTALLBIN=/software/varinf/bin
 STLPORT_INC=/software/solexa/pkg/STLport/current/stlport
 STLPORT_LIB=/software/solexa/pkg/STLport/current/build/lib/obj/gcc/so
+#STLPORT_INC=/software/varinf/lib/STLport/include/stlport
+#STLPORT_LIB=/software/varinf/lib/STLport/lib
 PERL_CORE=/usr/lib/perl/5.8.8/CORE
 PERL_CORE=/software/perl-5.8.8/lib/5.8.8/x86_64-linux-thread-multi/CORE
 
@@ -91,11 +93,11 @@ manifest: manifest.o Manifest.o
 g2i: g2i.o Gtc.o Manifest.o win2unix.o Sim.o json/json_reader.o json/json_writer.o json/json_value.o utilities.o plink_binary.o
 	$(CC) $(LDFLAGS) -o $@ $^ -lstlport
 
-#b2i: b2i.o Manifest.o b2base.o             # "b2" code needs ssl library;
-#	$(CC) $(LDFLAGS) -lssl  -o $@ $^ -lstlport       # pick this up from /usr/lib
+b2i: b2i.o Manifest.o b2base.o             # "b2" code needs ssl library;
+	$(CC) $(LDFLAGS) -lssl  -o $@ $^ -lstlport -lssl       # pick this up from /usr/lib
 
-#b2g: b2g.o Manifest.o b2base.o
-#	$(CC) $(LDFLAGS) -lssl -o $@ $^ -lstlport       # Ditto.
+b2g: b2g.o Manifest.o b2base.o
+	$(CC) $(LDFLAGS) -lssl -o $@ $^ -lstlport -lssl      # Ditto.
 
 gtc_process: Gtc.o Manifest.o gtc_process.o 
 	$(CC) $(LDFLAGS) -o $@ $^ -lstlport

Sim.cpp

@@ -68,12 +68,13 @@ void Sim::open(string fname)
 	magic = buff;
 
 	this->filename = fname;
-	infile->read(buff,1); version = *(uint8_t*)buff;
-	infile->read(buff,2); sampleNameSize = *(uint16_t*)buff;
-	infile->read(buff,4); numSamples = *(uint32_t*)buff;
-	infile->read(buff,4); numProbes = *(uint32_t*)buff;
-	infile->read(buff,1); numChannels = *(uint8_t*)buff;
-	infile->read(buff,1); numberFormat = *(uint8_t*)buff;
+	// read SIM header
+	infile->read((char*)&version,1);
+	infile->read((char*)&sampleNameSize,2);
+	infile->read((char*)&numSamples,4);
+	infile->read((char*)&numProbes,4);
+	infile->read((char*)&numChannels,1);
+	infile->read((char*)&numberFormat,1);
 
 	// calculate and store record length
 	recordLength = numProbes * numChannels;

g2i.cpp

@@ -59,8 +59,6 @@
 
 using namespace std;
 
-Json::Value root;   // will contains the root value after parsing.
-Json::Reader reader;
 
 hash_map<string,string> gtcHash;	// <sample_name, filename>
 Manifest *manifest = new Manifest();
@@ -483,7 +481,6 @@ void createBedFile(string fname, vector<string>infiles)
 			}
 			genotypes.push_back(call);
 		}
-		if (verbose) cerr << "SNP Count = " << pb->snps.size() << endl;
 		pb->write_individual(genotypes);
 		genotypes.clear();
 	}
@@ -777,21 +774,24 @@ int main(int argc, char *argv[])
 				case 'i':	ifstream f; string s;
 							f.open(optarg);
 							if (strstr(optarg,".json")) {
+								Json::Value root;   // will contains the root value after parsing.
+								Json::Reader reader;
 								bool parsingSuccessful = reader.parse( f, root );
 								if ( !parsingSuccessful ) {
 									std::cout  << "Failed to parse json file\n" << reader.getFormatedErrorMessages() << endl;
 									return 0;
 								}
 								for ( unsigned int index = 0; index < root.size(); ++index ) { // Iterates over the sequence elements.
 									sampleNames.push_back(root[index]["uri"].asString());
-//									cerr << "Gender Code = [" << root[index]["gender_code"] << "]" << endl;
 									char buffer[8];
-//									if (root[index]["gender_code"]) sprintf(buffer,"%d",root[index]["gender_code"].asInt());
-//									else                            strcpy(buffer,"-9");
 									sprintf(buffer,"%d",root[index]["gender_code"].asInt());
 									gender_code.push_back(buffer);
 									infiles.push_back(root[index]["result"].asString());
-cerr << root[index]["uri"].asString() << "\t" << root[index]["result"].asString() << "\t" << root[index]["gender_code"].asInt() << endl;
+									if (verbose) {
+										cerr << root[index]["uri"].asString() << "\t" 
+										     << root[index]["result"].asString() << "\t" 
+										     << root[index]["gender_code"].asInt() << endl;
+										}
 								}
 							} else {
 								while (f >> s) infiles.push_back(s);