From 52caf79395fcc5d7b28276aaab1f3e8ba2fce5c4 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 12 Jul 2017 10:42:19 -0400 Subject: [PATCH] r175: halved max-chain-skip in the ava mode --- main.c | 10 +++++----- map.c | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/main.c b/main.c index e562756..ff0476b 100644 --- a/main.c +++ b/main.c @@ -10,7 +10,7 @@ #include "minimap.h" #include "mmpriv.h" -#define MM_VERSION "2.0-r174-pre" +#define MM_VERSION "2.0-r175-pre" void liftrlimit() { @@ -126,11 +126,11 @@ int main(int argc, char *argv[]) } else if (c == 'x') { if (strcmp(optarg, "ava-ont") == 0) { opt.flag |= MM_F_AVA | MM_F_NO_SELF; - opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.min_seedcov_ratio = 0.05f, opt.max_gap = 10000; + opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.min_seedcov_ratio = 0.05f, opt.max_gap = 10000, opt.max_chain_skip = 25; k = 15, w = 5; } else if (strcmp(optarg, "ava-pb") == 0) { opt.flag |= MM_F_AVA | MM_F_NO_SELF; - opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.min_seedcov_ratio = 0.05f, opt.max_gap = 10000; + opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.min_seedcov_ratio = 0.05f, opt.max_gap = 10000, opt.max_chain_skip = 25; is_hpc = 1, k = 19, w = 5; } else if (strcmp(optarg, "map10k") == 0) { is_hpc = 1, k = 19; @@ -165,8 +165,8 @@ int main(int argc, char *argv[]) fprintf(stderr, " -N INT retain at most INT secondary alignments [%d]\n", opt.best_n); fprintf(stderr, " -D FLOAT min fraction of minimizer matches [%g]\n", opt.min_seedcov_ratio); fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n"); - fprintf(stderr, " ava-pb: -Hk19 -w5 -Xp0 -m100 -D.05 -g10000 (PacBio read overlap)\n"); - fprintf(stderr, " ava-ont: -k15 -w5 -Xp0 -m100 -D.05 -g10000 (ONT read overlap)\n"); + fprintf(stderr, " ava-pb: -Hk19 -w5 -Xp0 -m100 -D.05 -g10000 --max-chain-skip 25 (PacBio read overlap)\n"); + fprintf(stderr, " ava-ont: -k15 -w5 -Xp0 -m100 -D.05 -g10000 --max-chain-skip 25 (ONT read overlap)\n"); fprintf(stderr, " map10k: -Hk19 (PacBio/ONT vs reference mapping)\n"); fprintf(stderr, " asm1m: -k19 -w19 (intra-species assembly to ref mapping)\n"); fprintf(stderr, " Alignment:\n"); diff --git a/map.c b/map.c index f883632..3ddac1f 100644 --- a/map.c +++ b/map.c @@ -19,7 +19,7 @@ void mm_mapopt_init(mm_mapopt_t *opt) opt->min_chain_score = 40; opt->bw = 500; opt->max_gap = 5000; - opt->max_chain_skip = 50; + opt->max_chain_skip = 25; opt->min_seedcov_ratio = 0.0f; opt->mask_level = 0.5f;