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r175: halved max-chain-skip in the ava mode

This commit is contained in:
Heng Li 2017-07-12 10:42:19 -04:00
parent eeeb2ffb68
commit 52caf79395
2 changed files with 6 additions and 6 deletions
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10
main.c
View File

@ -10,7 +10,7 @@
#include "minimap.h" #include "minimap.h"
#include "mmpriv.h" #include "mmpriv.h"
#define MM_VERSION "2.0-r174-pre" #define MM_VERSION "2.0-r175-pre"
void liftrlimit() void liftrlimit()
{ {
@ -126,11 +126,11 @@ int main(int argc, char *argv[])
} else if (c == 'x') { } else if (c == 'x') {
if (strcmp(optarg, "ava-ont") == 0) { if (strcmp(optarg, "ava-ont") == 0) {
opt.flag |= MM_F_AVA | MM_F_NO_SELF; 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; k = 15, w = 5;
} else if (strcmp(optarg, "ava-pb") == 0) { } else if (strcmp(optarg, "ava-pb") == 0) {
opt.flag |= MM_F_AVA | MM_F_NO_SELF; 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; is_hpc = 1, k = 19, w = 5;
} else if (strcmp(optarg, "map10k") == 0) { } else if (strcmp(optarg, "map10k") == 0) {
is_hpc = 1, k = 19; 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, " -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, " -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, " -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-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 (ONT 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, " map10k: -Hk19 (PacBio/ONT vs reference mapping)\n");
fprintf(stderr, " asm1m: -k19 -w19 (intra-species assembly to ref mapping)\n"); fprintf(stderr, " asm1m: -k19 -w19 (intra-species assembly to ref mapping)\n");
fprintf(stderr, " Alignment:\n"); fprintf(stderr, " Alignment:\n");

2
map.c
View File

@ -19,7 +19,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->min_chain_score = 40; opt->min_chain_score = 40;
opt->bw = 500; opt->bw = 500;
opt->max_gap = 5000; opt->max_gap = 5000;
opt->max_chain_skip = 50; opt->max_chain_skip = 25;
opt->min_seedcov_ratio = 0.0f; opt->min_seedcov_ratio = 0.0f;
opt->mask_level = 0.5f; opt->mask_level = 0.5f;