diff --git a/bwamem.c b/bwamem.c index 00e0cc1..b9cdd82 100644 --- a/bwamem.c +++ b/bwamem.c @@ -67,7 +67,7 @@ mem_opt_t *mem_opt_init() o->split_factor = 1.5; o->chunk_size = 10000000; o->n_threads = 1; - o->max_hits = 10; + o->max_hits = 5; o->max_matesw = 50; o->mask_level_redun = 0.95; o->min_chain_weight = 0; diff --git a/fastmap.c b/fastmap.c index 3156ca3..cc5c1af 100644 --- a/fastmap.c +++ b/fastmap.c @@ -53,7 +53,7 @@ int main_mem(int argc, char *argv[]) opt = mem_opt_init(); memset(&opt0, 0, sizeof(mem_opt_t)); - while ((c = getopt(argc, argv, "epaFMCSPHYk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:")) >= 0) { + while ((c = getopt(argc, argv, "epaFMCSPHYk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:")) >= 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; @@ -76,6 +76,7 @@ int main_mem(int argc, char *argv[]) else if (c == 'r') opt->split_factor = atof(optarg), opt0.split_factor = 1.; else if (c == 'D') opt->drop_ratio = atof(optarg), opt0.drop_ratio = 1.; else if (c == 'm') opt->max_matesw = atoi(optarg), opt0.max_matesw = 1; + else if (c == 'h') opt->max_hits = atoi(optarg), opt0.max_hits = 1; else if (c == 's') opt->split_width = atoi(optarg), opt0.split_width = 1; else if (c == 'G') opt->max_chain_gap = atoi(optarg), opt0.max_chain_gap = 1; else if (c == 'N') opt->max_chain_extend = atoi(optarg), opt0.max_chain_extend = 1; diff --git a/main.c b/main.c index 3505ce7..7a05e80 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.8-r748-dirty" +#define PACKAGE_VERSION "0.7.8-r749-dirty" #endif int bwa_fa2pac(int argc, char *argv[]);