diff --git a/bwamem.c b/bwamem.c index 95478a6..71bf387 100644 --- a/bwamem.c +++ b/bwamem.c @@ -59,7 +59,7 @@ mem_opt_t *mem_opt_init() o->pen_unpaired = 17; o->pen_clip5 = o->pen_clip3 = 5; - o->max_mem_intv = 0; + o->max_mem_intv = 10; o->min_seed_len = 19; o->split_width = 10; diff --git a/fastmap.c b/fastmap.c index e949da3..ddf464a 100644 --- a/fastmap.c +++ b/fastmap.c @@ -145,7 +145,7 @@ int main_mem(int argc, char *argv[]) fprintf(stderr, " -w INT band width for banded alignment [%d]\n", opt->w); fprintf(stderr, " -d INT off-diagonal X-dropoff [%d]\n", opt->zdrop); fprintf(stderr, " -r FLOAT look for internal seeds inside a seed longer than {-k} * FLOAT [%g]\n", opt->split_factor); - fprintf(stderr, " -y INT find MEMs longer than {-k} * {-r} with size less than INT (EXPERIMENTAL) [%ld]\n", (long)opt->max_mem_intv); + fprintf(stderr, " -y INT seed occurrence for the 3rd round seeding [%ld]\n", (long)opt->max_mem_intv); // fprintf(stderr, " -s INT look for internal seeds inside a seed with less than INT occ [%d]\n", opt->split_width); fprintf(stderr, " -c INT skip seeds with more than INT occurrences [%d]\n", opt->max_occ); fprintf(stderr, " -D FLOAT drop chains shorter than FLOAT fraction of the longest overlapping chain [%.2f]\n", opt->drop_ratio); diff --git a/main.c b/main.c index 54f93fe..e8fb688 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.10-r929-dirty" +#define PACKAGE_VERSION "0.7.10-r930-dirty" #endif int bwa_fa2pac(int argc, char *argv[]);