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Copy pathoptions.c
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122 lines (118 loc) · 3.29 KB
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#include <string.h>
#include <math.h>
#include "minibwa.h"
static void mb_opt_reset(mb_opt_t *opt)
{
memset(opt, 0, sizeof(mb_opt_t));
opt->min_len = 19;
opt->max_sr_len = 325;
// seeding options
opt->max_sub_occ = 10;
opt->min_sub_occ = 1;
opt->max_occ = 250;
// chaining options
opt->max_chain_skip = 25;
opt->max_chain_iter = 5000;
opt->chain_gap_scale = 0.8f;
opt->bw_long = 20000;
opt->pri_ratio = 0.5f;
// hit processing options
opt->mask_level = 0.5f;
opt->mask_len = 0x7fffffff;
opt->lift_tol = MB_LIFT_TOL;
// alignment options
opt->a = 2, opt->b = 8;
opt->q = 12, opt->q2 = 23;
opt->e = 2, opt->e2 = 1;
opt->b_ambi = 1;
/* Default 0 to preserve historical minibwa extend/clip behavior; bwa-mem
* default is 5,5 but enabling that as the minibwa default would shift
* existing alignments unannounced. */
opt->pen_clip5 = opt->pen_clip3 = 0;
// pairing options
opt->max_pe_ins = 10000;
opt->max_rescue = 10;
opt->pen_unpair = 17;
opt->pe_avg = 400, opt->pe_std = 100;
opt->pe_lo = 50, opt->pe_hi = 800;
// I/O options
opt->sb_len = 1000000;
opt->sb_seq = 24;
opt->n_thread = 1;
opt->seed = 11;
opt->out_s = 0.8f;
opt->xa_max = 5;
opt->meth_tags = MB_METH_TAG_ALL;
opt->max_sw_mat = 100000000;
opt->cap_kalloc = 1UL<<28;
opt->max_mb_size = 1000000000;
#ifndef HAVE_KALLOC
opt->flag |= MB_F_NO_KALLOC;
#endif
}
void mb_opt_init(mb_opt_t *opt)
{
mb_opt_reset(opt);
mb_opt_preset(opt, "adap");
}
int mb_opt_preset(mb_opt_t *opt, const char *preset)
{
mb_opt_reset(opt);
if (strcmp(preset, "sr") == 0 || strcmp(preset, "adap") == 0) {
opt->flag |= MB_F_PE;
if (strcmp(preset, "adap") == 0) opt->flag |= MB_F_ADAP;
opt->min_dp_max = 30;
opt->bw = 100;
opt->max_gap = 100;
opt->zdrop = 80;
opt->zdrop_inv = 80;
opt->best_n = 50;
opt->end_bonus = 10;
opt->min_chain_score = 25;
opt->min_ksw_len = 20;
opt->mb_size = 100000000;
} else if (strcmp(preset, "lr") == 0) {
opt->flag |= MB_F_LONG;
opt->flag &= ~MB_F_PE;
opt->min_dp_max = 50;
opt->bw = 500;
opt->max_gap = 5000;
opt->zdrop = 400;
opt->zdrop_inv = 240;
opt->best_n = 5;
opt->end_bonus = -1;
opt->min_chain_score = 40;
opt->min_ksw_len = 200;
opt->mb_size = 500000000;
} else {
return -1;
}
return 0;
}
void mb_opt_adap(const mb_opt_t *opt0, int32_t len, mb_opt_t *opt)
{
const int32_t min_len = 100, mid_len = 2000;
double a, b;
*opt = *opt0;
if (!(opt0->flag & MB_F_ADAP)) return;
a = -log(0.5) / (mid_len - min_len);
b = exp(-a * ((len > min_len? len : min_len) - min_len));
if (opt0->max_gap < 5000) {
opt->max_gap = (int32_t)(5000 - (5000 - opt0->max_gap) * b + .499);
if (opt->max_gap > len) opt->max_gap = len;
}
if (opt0->bw < 500)
opt->bw = (int32_t)(500 - (500 - opt0->bw) * b + .499);
if (opt->bw_long > len * 5) opt->bw_long = len * 5;
if (opt->bw_long < opt->bw) opt->bw_long = opt->bw;
if (opt0->zdrop < 400)
opt->zdrop = (int32_t)(400 - (400 - opt0->zdrop) * b + .499);
if (opt0->zdrop_inv < 240)
opt->zdrop_inv = (int32_t)(240 - (240 - opt0->zdrop_inv) * b + .499);
if (opt0->best_n > 5)
opt->best_n = (int32_t)((opt0->best_n - 5) * b + 5 + .499);
if (opt0->min_dp_max < 50)
opt->min_dp_max = (int32_t)(50 - (50 - opt0->min_dp_max) * b + .499);
if (opt0->min_chain_score < 40)
opt->min_chain_score = (int32_t)(40 - (40 - opt0->min_chain_score) * b + .499);
}