fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-01 06:48:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

r1183: added lr:hq; fixed transition

Browse Source 
* Added the lr:hq preset suggested by Nanopore developers (#1127)
 * Fixed transition scoring. It did not work with presets.
 * Cleaned up preset documentation
This commit is contained in:
Heng Li
2024-03-10 13:47:34 -04:00
parent bc588c0eeb
commit 8140259974
5 changed files with 73 additions and 29 deletions
Download Patch File Download Diff File Expand all files Collapse all files
options.c
+8 -7
View File
@@ -45,7 +45,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->alt_drop = 0.15f;
opt->a = 2, opt->b = 4, opt->q = 4, opt->e = 2, opt->q2 = 24, opt->e2 = 1;
opt->transition = opt->b;
opt->transition = 0;
opt->sc_ambi = 1;
opt->zdrop = 400, opt->zdrop_inv = 200;
opt->end_bonus = -1;
@@ -91,7 +91,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
if (preset == 0) {
mm_idxopt_init(io);
mm_mapopt_init(mo);
} else if (strcmp(preset, "map-ont") == 0) { // this is the same as the default
} else if (strcmp(preset, "lr") == 0 || strcmp(preset, "map-ont") == 0) { // this is the same as the default
} else if (strcmp(preset, "ava-ont") == 0) {
io->flag = 0, io->k = 15, io->w = 5;
mo->flag |= MM_F_ALL_CHAINS | MM_F_NO_DIAG | MM_F_NO_DUAL | MM_F_NO_LJOIN;
@@ -106,13 +106,14 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->min_chain_score = 100, mo->pri_ratio = 0.0f, mo->max_chain_skip = 25;
mo->bw_long = mo->bw;
mo->occ_dist = 0;
} else if (strcmp(preset, "map-hifi") == 0 || strcmp(preset, "map-ccs") == 0) {
} else if (strcmp(preset, "lr:hq") == 0 || strcmp(preset, "map-hifi") == 0 || strcmp(preset, "map-ccs") == 0) {
io->flag = 0, io->k = 19, io->w = 19;
mo->max_gap = 10000;
mo->a = 1, mo->b = 4, mo->q = 6, mo->q2 = 26, mo->e = 2, mo->e2 = 1;
mo->occ_dist = 500;
mo->min_mid_occ = 50, mo->max_mid_occ = 500;
mo->min_dp_max = 200;
if (strcmp(preset, "map-hifi") == 0 || strcmp(preset, "map-ccs") == 0) {
mo->a = 1, mo->b = 4, mo->q = 6, mo->q2 = 26, mo->e = 2, mo->e2 = 1;
mo->min_dp_max = 200;
}
} else if (strcmp(preset, "map-iclr-prerender") == 0) {
io->flag = 0, io->k = 15;
mo->b = 6, mo->transition = 1;
@@ -165,7 +166,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->junc_bonus = 9;
mo->zdrop = 200, mo->zdrop_inv = 100; // because mo->a is halved
if (strcmp(preset, "splice:hq") == 0)
mo->junc_bonus = 5, mo->b = 4, mo->q = 6, mo->q2 = 24;
mo->noncan = 5, mo->b = 4, mo->q = 6, mo->q2 = 24;
} else return -1;
return 0;
}