Proper Gzip check

src/utils/bedFile/bedFile.cpp

@@ -135,7 +135,7 @@ void BedFile::Open(void) {
     else {
         _bedStream = new ifstream(bedFile.c_str(), ios::in);
         
-        if(bedFile.substr(bedFile.find_last_of(".") + 1) == "gz") {
+        if( isGzipFile(_bedStream) ) {
             delete _bedStream;
             _bedStream = new igzstream(bedFile.c_str(), ios::in);
         }

src/utils/bedFilePE/bedFilePE.cpp

@@ -35,10 +35,6 @@ void BedFilePE::Open(void) {
             delete _bedStream;
             _bedStream = new igzstream(bedFile.c_str(), ios::in);
         }
-        
-        // bytes were consumed.  rewind.
-        _bedStream->seekg(0);
-        
         // can we open the file?
         if ( !(_bedStream->good()) ) {
             cerr << "Error: The requested bed file (" << bedFile << ") could not be opened. Exiting!" << endl;
@@ -48,6 +44,7 @@ void BedFilePE::Open(void) {
 }
 
 
+
 // Close the BEDPE file
 void BedFilePE::Close(void) {
     if (bedFile != "stdin") delete _bedStream;

src/utils/bedGraphFile/bedGraphFile.cpp

@@ -37,10 +37,6 @@ void BedGraphFile::Open() {
             delete _bedGraphStream;
             _bedGraphStream = new igzstream(bedGraphFile.c_str(), ios::in);
         }
-        
-        // bytes were consumed.  rewind.
-        _bedGraphStream->seekg(0);
-        
         // can we open the file?
         if ( !(_bedGraphStream->good()) ) {
             cerr << "Error: The requested bed file (" << bedGraphFile << ") could not be opened. Exiting!" << endl;