Adding control cs improvement

cpp/Vihgo.cpp

@@ -990,11 +990,16 @@ int Vihgo::readRunControl()
 					int a = bam_seqi( sequence , i+x );
 					char base;
 					base = this->getBase( a );
-
 					codon += base;
 				}
 				i += 2;
 
+				if (codon.find( "!" ) != string::npos )
+				{
+					continue;
+				}
+
+
 				// insert the codon in the data
 				if( !( this->sampleData.count( chr ) > 0) )
 				{
@@ -1659,6 +1664,12 @@ int Vihgo::readSample()
 				}
 				i += 2;
 
+				if (codon.find( "!" ) != string::npos )
+				{
+					continue;
+				}
+
+
 				// insert the codon in the data
 				if( !( this->sampleData.count( chr ) > 0) )
 				{
@@ -1979,6 +1990,7 @@ bool Vihgo::isThereAControl()
 
 char Vihgo::getBase( int b )
 {
+	// cerr << "inc int base: " << b << " : " << endl;;
 	switch( b )
 	{
 		case 1 :
@@ -1996,6 +2008,6 @@ char Vihgo::getBase( int b )
 		case 15 :
 			return 'N';
 	}
-	return 'N';
+	return '!';
 }
 // setters