compilation fix

src/snpCaller/call_vC.cpp

@@ -53,7 +53,7 @@ static int print_usage()
   fprintf(stderr, "Contact: Paul Costea <costea@embl.de>,\n\t Robin Muench <rmuench@embl.de>\n\n");
   fprintf(stderr, "Usage:   snpCall [options] <stdin.mpileup> \n");
   fprintf(stderr, "Options: \n");
-  fprintf(stderr, "	    -b,		TODO: list of input BAM filenames, one per line (for header) \n ");
+//  fprintf(stderr, "	    -b,		TODO: list of input BAM filenames, one per line (for header) \n ");
   fprintf(stderr, "	    -f,		faidx indexed reference metagenome \n ");
   fprintf(stderr, "	    -g,		gene annotation file [NULL].\n");
   fprintf(stderr, "	    -i,		individual SNPs output file [NULL].\n\n");
@@ -603,7 +603,7 @@ std::map<std::string, char> CodonMap(codons, codons + sizeof codons / sizeof cod
             sToWrite = &s;
         } else { //May be a individual variant
             for (int i=1; i<=nrSamples; ++i) {
-                int s = getSum(map,snp,i);
+                int s = getSum(map,check,i);
                 if (s >= CALLING_THRESHOLD) {//We observe the variant "CALLING_THRESHOLD" times in one sample.
                     writeThis = true;
     	            sToWrite = &indiv;