From 71e2a97a4c58e4abebb77b856aaa19285573d29c Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 18 Jul 2017 00:00:36 -0400 Subject: [PATCH] r180: changed -x asm5 settings --- main.c | 12 +++++++----- map.c | 2 +- minimap2.1 | 4 ++-- 3 files changed, 10 insertions(+), 8 deletions(-) diff --git a/main.c b/main.c index b19da7a..a9c3ca2 100644 --- a/main.c +++ b/main.c @@ -10,7 +10,7 @@ #include "minimap.h" #include "mmpriv.h" -#define MM_VERSION "2.0-r179-pre" +#define MM_VERSION "2.0-r180-pre" void liftrlimit() { @@ -50,6 +50,7 @@ static struct option long_options[] = { { "no-self", no_argument, 0, 0 }, { "print-seed", no_argument, 0, 0 }, { "max-chain-skip", required_argument, 0, 0 }, + { "min-dp-len", required_argument, 0, 0 }, { "version", no_argument, 0, 'V' }, { "min-count", required_argument, 0, 'n' }, { "min-chain-score",required_argument, 0, 'm' }, @@ -104,6 +105,7 @@ int main(int argc, char *argv[]) else if (c == 0 && long_idx == 5) opt.flag |= MM_F_NO_SELF; // --no-self else if (c == 0 && long_idx == 6) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_SEED; // --print-seed else if (c == 0 && long_idx == 7) opt.max_chain_skip = atoi(optarg); // --max-chain-skip + else if (c == 0 && long_idx == 8) opt.min_ksw_len = atoi(optarg); // --min-dp-len else if (c == 'V') { puts(MM_VERSION); return 0; @@ -137,11 +139,11 @@ int main(int argc, char *argv[]) is_hpc = 1, k = 19; } else if (strcmp(optarg, "asm5") == 0) { k = 19, w = 19; - opt.a = 1, opt.b = 19, opt.q = 39, opt.q2 = 61, opt.e = 2, opt.e2 = 1; + opt.a = 1, opt.b = 19, opt.q = 39, opt.q2 = 81, opt.e = 3, opt.e2 = 1, opt.zdrop = 200; opt.min_dp_max = 200; } else if (strcmp(optarg, "asm10") == 0) { k = 19, w = 19; - opt.a = 1, opt.b = 9, opt.q = 16, opt.q2 = 41, opt.e = 2, opt.e2 = 1; + opt.a = 1, opt.b = 9, opt.q = 16, opt.q2 = 41, opt.e = 2, opt.e2 = 1, opt.zdrop = 200; opt.min_dp_max = 200; } else { fprintf(stderr, "[E::%s] unknown preset '%s'\n", __func__, optarg); @@ -174,8 +176,8 @@ int main(int argc, char *argv[]) fprintf(stderr, " ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (PacBio read overlap)\n"); fprintf(stderr, " ava-ont: -k15 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (ONT read overlap)\n"); fprintf(stderr, " map10k: -Hk19 (PacBio/ONT vs reference mapping)\n"); - fprintf(stderr, " asm5: -k19 -w19 -A1 -B19 -O39,61 -E2,1 -s200 (assembly to ref mapping; break at 5%% div.)\n"); - fprintf(stderr, " asm10: -k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 (assembly to ref mapping; break at 10%% div.)\n"); + fprintf(stderr, " asm5: -k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 (asm to ref mapping; break at 5%% div.)\n"); + fprintf(stderr, " asm10: -k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 (asm to ref mapping; break at 10%% div.)\n"); fprintf(stderr, " Alignment:\n"); fprintf(stderr, " -A INT matching score [%d]\n", opt.a); fprintf(stderr, " -B INT mismatch penalty [%d]\n", opt.b); diff --git a/map.c b/map.c index 845aa6d..0d20057 100644 --- a/map.c +++ b/map.c @@ -32,7 +32,7 @@ void mm_mapopt_init(mm_mapopt_t *opt) opt->a = 2, opt->b = 4, opt->q = 4, opt->e = 2, opt->q2 = 24, opt->e2 = 1; opt->zdrop = 400; opt->min_dp_max = opt->min_chain_score; - opt->min_ksw_len = 100; + opt->min_ksw_len = 200; } void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi) diff --git a/minimap2.1 b/minimap2.1 index 4e60b22..8626a0e 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -184,12 +184,12 @@ Oxford Nanopore all-vs-all overlap mapping (-k15 -w5 -Xp0 -m100 -K500m -g10000 - PacBio/Oxford Nanopore read to reference mapping (-Hk19) .TP .B asm5 -Long assembly to reference mapping (-k19 -w19 -A1 -B19 -O39,61 -E2,1 -s200). +Long assembly to reference mapping (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200). 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%. .TP .B asm10 -Long assembly to reference mapping (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200). Up +Long assembly to reference mapping (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200). Up to 10% sequence divergence. .RE .TP