diff --git a/main.c b/main.c index 900bd08..1455ca0 100644 --- a/main.c +++ b/main.c @@ -7,7 +7,7 @@ #include "mmpriv.h" #include "ketopt.h" -#define MM_VERSION "2.23-r1117-dirty" +#define MM_VERSION "2.23-r1118-dirty" #ifdef __linux__ #include diff --git a/minimap2.1 b/minimap2.1 index 7d0c2c5..666de78 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -565,7 +565,7 @@ Align older PacBio continuous long (CLR) reads to a reference genome .B asm5 Long assembly to reference mapping .RB ( -k19 -.B -w19 -U50,500 --rmq -r100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200 +.B -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200 .BR -N50 ). Typically, the alignment will not extend to regions with 5% or higher sequence divergence. Only use this preset if the average divergence is far below 5%. @@ -573,14 +573,14 @@ divergence. Only use this preset if the average divergence is far below 5%. .B asm10 Long assembly to reference mapping .RB ( -k19 -.B -w19 -U50,500 --rmq -r100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200 +.B -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200 .BR -N50 ). Up to 10% sequence divergence. .TP .B asm20 Long assembly to reference mapping .RB ( -k19 -.B -w10 -U50,500 --rmq -r100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200 +.B -w10 -U50,500 --rmq -r1k,100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200 .BR -N50 ). Up to 20% sequence divergence. .TP diff --git a/options.c b/options.c index 285c57b..18aafdc 100644 --- a/options.c +++ b/options.c @@ -113,7 +113,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo) mo->min_dp_max = 200; } else if (strncmp(preset, "asm", 3) == 0) { io->flag = 0, io->k = 19, io->w = 19; - mo->bw = mo->bw_long = 100000; + mo->bw = 1000, mo->bw_long = 100000; mo->max_gap = 10000; mo->flag |= MM_F_RMQ; mo->min_mid_occ = 50, mo->max_mid_occ = 500;