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redesigned indexing and option APIs

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This commit is contained in:
Heng Li
2017-09-14 17:02:01 -04:00
parent 0f7455cefa
commit eb00521d9b
5 changed files with 151 additions and 98 deletions
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map.c
+51 -2
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@@ -34,6 +34,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->zdrop = 400;
opt->min_dp_max = opt->min_chain_score * opt->a;
opt->min_ksw_len = 200;
opt->mini_batch_size = 200000000;
}
void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
@@ -49,6 +50,54 @@ void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
opt->mid_occ, opt->max_occ);
}
int mm_preset(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
{
if (strcmp(preset, "ava-ont") == 0) {
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) {
io->is_hpc = 0, io->k = 15;
} else if (strcmp(preset, "asm5") == 0) {
io->is_hpc = 0, io->k = 19, io->w = 19;
mo->a = 1, mo->b = 19, mo->q = 39, mo->q2 = 81, mo->e = 3, mo->e2 = 1, mo->zdrop = 200;
mo->min_dp_max = 200;
} else if (strcmp(preset, "asm10") == 0) {
io->is_hpc = 0, io->k = 19, io->w = 19;
mo->a = 1, mo->b = 9, mo->q = 16, mo->q2 = 41, mo->e = 2, mo->e2 = 1, mo->zdrop = 200;
mo->min_dp_max = 200;
} else if (strcmp(preset, "short") == 0 || strcmp(preset, "sr") == 0) {
io->is_hpc = 0, io->k = 21, io->w = 11;
mo->flag |= MM_F_APPROX_EXT;
mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 32, mo->e2 = 1;
mo->max_gap = 100;
mo->pri_ratio = 0.5f;
mo->min_cnt = 2;
mo->min_chain_score = 20;
mo->min_dp_max = 40;
mo->best_n = 20;
mo->bw = 50;
mo->mid_occ = 1000;
mo->mini_batch_size = 50000000;
} else if (strcmp(preset, "splice") == 0 || strcmp(preset, "cdna") == 0) {
io->is_hpc = 0, io->k = 15, io->w = 5;
mo->flag |= MM_F_SPLICE | MM_F_SPLICE_FOR | MM_F_SPLICE_REV;
mo->max_gap = 2000, mo->max_gap_ref = mo->bw = 200000;
mo->a = 1, mo->b = 2, mo->q = 2, mo->e = 1, mo->q2 = 32, mo->e2 = 0;
mo->noncan = 5;
mo->zdrop = 200;
} else return -1;
return 0;
}
typedef struct {
uint32_t n;
uint32_t qpos;
@@ -304,7 +353,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
return 0;
}
int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int n_threads, int mini_batch_size)
int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int n_threads)
{
pipeline_t pl;
memset(&pl, 0, sizeof(pipeline_t));
@@ -315,7 +364,7 @@ int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int
return -1;
}
pl.opt = opt, pl.mi = idx;
pl.n_threads = n_threads, pl.mini_batch_size = mini_batch_size;
pl.n_threads = n_threads, pl.mini_batch_size = opt->mini_batch_size;
if ((opt->flag & MM_F_OUT_SAM) && !(opt->flag & MM_F_NO_SAM_SQ))
mm_write_sam_SQ(idx);
kt_pipeline(n_threads == 1? 1 : 2, worker_pipeline, &pl, 3);