fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-09-24 08:08:13 +08:00
Code Issues Packages Projects Releases Wiki Activity

r518: increased the default -K to 500M

Browse Source 
This helps multi-thread performance for ultra-long reads.
This commit is contained in:
Heng Li
2017-10-17 13:21:29 -04:00
parent 25ffd72690
commit 04cf4ebf5e
3 changed files with 10 additions and 17 deletions
Download Patch File Download Diff File Expand all files Collapse all files
map.c
+1 -3
View File
@@ -36,7 +36,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->end_bonus = -1;
opt->min_dp_max = opt->min_chain_score * opt->a;
opt->min_ksw_len = 200;
opt->mini_batch_size = 200000000;
opt->mini_batch_size = 500000000;
opt->pe_ori = 0; // FF
opt->pe_bonus = 33;
@@ -61,12 +61,10 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
io->is_hpc = 0, io->k = 15, io->w = 5;
mo->flag |= MM_F_AVA | MM_F_NO_SELF;
mo->min_chain_score = 100, mo->pri_ratio = 0.0f, mo->max_gap = 10000, mo->max_chain_skip = 25;
mo->mini_batch_size = 500000000;
} else if (strcmp(preset, "ava-pb") == 0) {
io->is_hpc = 1, io->k = 19, io->w = 5;
mo->flag |= MM_F_AVA | MM_F_NO_SELF;
mo->min_chain_score = 100, mo->pri_ratio = 0.0f, mo->max_gap = 10000, mo->max_chain_skip = 25;
mo->mini_batch_size = 500000000;
} else if (strcmp(preset, "map10k") == 0 || strcmp(preset, "map-pb") == 0) {
io->is_hpc = 1, io->k = 19;
} else if (strcmp(preset, "map-ont") == 0) {