diff --git a/fastmap.c b/fastmap.c index 18f3b0e..25bf822 100644 --- a/fastmap.c +++ b/fastmap.c @@ -55,7 +55,7 @@ int main_mem(int argc, char *argv[]) opt = mem_opt_init(); memset(&opt0, 0, sizeof(mem_opt_t)); - while ((c = getopt(argc, argv, "epaFMCSPHVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:K:")) >= 0) { + while ((c = getopt(argc, argv, "epaFMCSPHVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:K:X:")) >= 0) { if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1; else if (c == 'x') mode = optarg; else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1; @@ -87,6 +87,7 @@ int main_mem(int argc, char *argv[]) else if (c == 'y') opt->max_mem_intv = atol(optarg), opt0.max_mem_intv = 1; else if (c == 'C') copy_comment = 1; else if (c == 'K') fixed_chunk_size = atoi(optarg); + else if (c == 'X') opt->mask_level = atof(optarg); else if (c == 'h') { opt0.max_XA_hits = opt0.max_XA_hits_alt = 1; opt->max_XA_hits = opt->max_XA_hits_alt = strtol(optarg, &p, 10); diff --git a/main.c b/main.c index f8f6995..a69ffeb 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.10-r960-dirty" +#define PACKAGE_VERSION "0.7.10-r963-dirty" #endif int bwa_fa2pac(int argc, char *argv[]);