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r573: prepare to generalize index

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Heng Li
2017-11-11 19:54:06 -05:00
parent 3b518271ee
commit 2f463b1db0
6 changed files with 38 additions and 35 deletions
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map.c
+9 -9
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@@ -64,29 +64,29 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mm_idxopt_init(io);
mm_mapopt_init(mo);
} else if (strcmp(preset, "ava-ont") == 0) {
io->is_hpc = 0, io->k = 15, io->w = 5;
io->flag = 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;
} else if (strcmp(preset, "ava-pb") == 0) {
io->is_hpc = 1, io->k = 19, io->w = 5;
io->flag |= MM_I_HPC, 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;
} else if (strcmp(preset, "map10k") == 0 || strcmp(preset, "map-pb") == 0) {
io->is_hpc = 1, io->k = 19;
io->flag |= MM_I_HPC, io->k = 19;
} else if (strcmp(preset, "map-ont") == 0) {
io->is_hpc = 0, io->k = 15;
io->flag = 0, io->k = 15;
} else if (strcmp(preset, "asm5") == 0) {
io->is_hpc = 0, io->k = 19, io->w = 19;
io->flag = 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;
mo->best_n = 50;
} else if (strcmp(preset, "asm10") == 0) {
io->is_hpc = 0, io->k = 19, io->w = 19;
io->flag = 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;
mo->best_n = 50;
} else if (strcmp(preset, "short") == 0 || strcmp(preset, "sr") == 0) {
io->is_hpc = 0, io->k = 21, io->w = 11;
io->flag = 0, io->k = 21, io->w = 11;
mo->flag |= MM_F_SR | MM_F_FRAG_MODE | MM_F_NO_PRINT_2ND | MM_F_2_IO_THREADS;
mo->pe_ori = 0<<1|1; // FR
mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 24, mo->e2 = 1;
@@ -104,7 +104,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->max_occ = 5000;
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;
io->flag = 0, io->k = 15, io->w = 5;
mo->flag |= MM_F_SPLICE | MM_F_SPLICE_FOR | MM_F_SPLICE_REV | MM_F_SPLICE_FLANK;
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;
@@ -173,7 +173,7 @@ static void collect_minimizers(const mm_mapopt_t *opt, const mm_idx_t *mi, int n
int i, j, n, sum = 0;
b->mini.n = 0;
for (i = n = 0; i < n_segs; ++i) {
mm_sketch(b->km, seqs[i], qlens[i], mi->w, mi->k, i, mi->is_hpc, &b->mini);
mm_sketch(b->km, seqs[i], qlens[i], mi->w, mi->k, i, mi->flag&MM_I_HPC, &b->mini);
for (j = n; j < b->mini.n; ++j)
b->mini.a[j].y += sum << 1;
if (opt->sdust_thres > 0) // mask low-complexity minimizers