fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-09-28 08:38:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

r190: default -k to 15; added -x map-ont

Browse Source
This commit is contained in:
Heng Li
2017-07-19 10:11:14 -04:00
parent 470021fd27
commit 4aff301ef4
2 changed files with 60 additions and 40 deletions
Download Patch File Download Diff File Expand all files Collapse all files
main.c
+13 -9
View File
@@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r189-dirty"
#define MM_VERSION "2.0-r190-dirty"
void liftrlimit()
{
@@ -63,7 +63,7 @@ static struct option long_options[] = {
int main(int argc, char *argv[])
{
mm_mapopt_t opt;
int i, c, k = 17, w = -1, bucket_bits = MM_IDX_DEF_B, n_threads = 3, keep_name = 1, is_idx, is_hpc = 0, long_idx;
int i, c, k = 15, w = -1, bucket_bits = MM_IDX_DEF_B, n_threads = 3, keep_name = 1, is_idx, is_hpc = 0, long_idx;
int minibatch_size = 200000000;
uint64_t batch_size = 4000000000ULL;
mm_bseq_file_t *fp = 0;
@@ -135,8 +135,10 @@ int main(int argc, char *argv[])
opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.max_gap = 10000, opt.max_chain_skip = 25;
minibatch_size = 500000000;
is_hpc = 1, k = 19, w = 5;
} else if (strcmp(optarg, "map10k") == 0) {
} else if (strcmp(optarg, "map10k") == 0 || strcmp(optarg, "map-pb") == 0) {
is_hpc = 1, k = 19;
} else if (strcmp(optarg, "map-ont") == 0) {
is_hpc = 0, k = 15;
} else if (strcmp(optarg, "asm5") == 0) {
k = 19, w = 19;
opt.a = 1, opt.b = 19, opt.q = 39, opt.q2 = 81, opt.e = 3, opt.e2 = 1, opt.zdrop = 200;
@@ -172,12 +174,6 @@ int main(int argc, char *argv[])
fprintf(stderr, " -X skip self and dual mappings (for the all-vs-all mode)\n");
fprintf(stderr, " -p FLOAT min secondary-to-primary score ratio [%g]\n", opt.pri_ratio);
fprintf(stderr, " -N INT retain at most INT secondary alignments [%d]\n", opt.best_n);
fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n");
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 -O39,81 -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);
@@ -193,6 +189,14 @@ int main(int argc, char *argv[])
fprintf(stderr, " -K NUM minibatch size [200M]\n");
// fprintf(stderr, " -v INT verbose level [%d]\n", mm_verbose);
fprintf(stderr, " -V show version number\n");
fprintf(stderr, " Preset:\n");
fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n");
fprintf(stderr, " map10k/map-pb: -Hk19 (PacBio/ONT vs reference mapping)\n");
fprintf(stderr, " map-ont: -k15 (slightly more sensitive than 'map10k' for ONT vs reference)\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, " 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, "\nSee `man ./minimap2.1' for detailed description of command-line options.\n");
return 1;
}