allow the user to specify the XA drop ratio via the -z option

fastmap.c

@@ -156,7 +156,7 @@ int main_mem(int argc, char *argv[])
 
 	aux.opt = opt = mem_opt_init();
 	memset(&opt0, 0, sizeof(mem_opt_t));
-	while ((c = getopt(argc, argv, "51qpaMCSPVYjuk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:o:f:W:x:G:h:y:K:X:H:")) >= 0) {
+	while ((c = getopt(argc, argv, "51qpaMCSPVYjuk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:o:f:W:x:G:h:y:K:X:H:z:")) >= 0) {
 		if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
 		else if (c == '1') no_mt_io = 1;
 		else if (c == 'x') mode = optarg;
@@ -198,6 +198,7 @@ int main_mem(int argc, char *argv[])
 			if (*p != 0 && ispunct(*p) && isdigit(p[1]))
 				opt->max_XA_hits_alt = strtol(p+1, &p, 10);
 		}
+		else if (c == 'z') opt->XA_drop_ratio = atof(optarg);
 		else if (c == 'Q') {
 			opt0.mapQ_coef_len = 1;
 			opt->mapQ_coef_len = atoi(optarg);
@@ -302,7 +303,12 @@ int main_mem(int argc, char *argv[])
 		fprintf(stderr, "\n");
 		fprintf(stderr, "       -v INT        verbosity level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose);
 		fprintf(stderr, "       -T INT        minimum score to output [%d]\n", opt->T);
-		fprintf(stderr, "       -h INT[,INT]  if there are <INT hits with score >80%% of the max score, output all in XA [%d,%d]\n", opt->max_XA_hits, opt->max_XA_hits_alt);
+		fprintf(stderr, "       -h INT[,INT]  if there are <INT hits with score >%.2f%% of the max score, output all in XA [%d,%d]\n", 
+				opt->XA_drop_ratio * 100.0,
+				opt->max_XA_hits, opt->max_XA_hits_alt);
+		fprintf(stderr, "                     A second value may be given for alternate sequences.\n");
+		fprintf(stderr, "       -z FLOAT      The fraction of the max score to use with -h [%f].\n", opt->XA_drop_ratio);
+		fprintf(stderr, "                     specify the mean, standard deviation (10%% of the mean if absent), max\n");
 		fprintf(stderr, "       -a            output all alignments for SE or unpaired PE\n");
 		fprintf(stderr, "       -C            append FASTA/FASTQ comment to SAM output\n");
 		fprintf(stderr, "       -V            output the reference FASTA header in the XR tag\n");