snpCaller options: SNP definitions

src/snpCaller/call_vC.cpp

@@ -65,7 +65,12 @@ static int print_usage()
   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");
+  fprintf(stderr, "SNP definition: \n"); 
+  fprintf(stderr, "	    -c, 	minimum coverage (mapped reads) per position [4]\n ");
+  fprintf(stderr, "	    -p, 	minimum non-reference nucleotide allele frequency per position [0.01].\n");
+  fprintf(stderr, "	    -t, 	minimum number of non-reference nucleotides per position [4].\n\n");
 //  fprintf(stderr, "	    -d,-a,	for debugging only \n\n");
+  fprintf(stderr, "\n");
   fprintf(stderr, "Note: Expecting samtools mpileup as standard input\n\n");
   return 1;
 }