compilable again
This commit is contained in:
Heng Li
parent
56723ad580
commit
de367a340c
2
index.c
2
index.c
|
|
@ -325,7 +325,7 @@ mm_idx_t *mm_idx_load(FILE *fp)
|
|||
|
||||
if (fread(magic, 1, 4, fp) != 4) return 0;
|
||||
if (strncmp(magic, MM_IDX_MAGIC, 4) != 0) return 0;
|
||||
if (fread(x, 4, 5, fp) != 6) return 0;
|
||||
if (fread(x, 4, 5, fp) != 5) return 0;
|
||||
mi = mm_idx_init(x[0], x[1], x[2], x[4]);
|
||||
mi->n_seq = x[3];
|
||||
mi->seq = (mm_idx_seq_t*)calloc(mi->n_seq, sizeof(mm_idx_seq_t));
|
||||
|
|
|
|||
12
main.c
12
main.c
|
|
@ -7,7 +7,7 @@
|
|||
#include "bseq.h"
|
||||
#include "minimap.h"
|
||||
|
||||
#define MM_VERSION "0.2-r124-dirty"
|
||||
#define MM_VERSION "2.0-r14-pre"
|
||||
|
||||
void liftrlimit()
|
||||
{
|
||||
|
|
@ -34,7 +34,7 @@ int main(int argc, char *argv[])
|
|||
mm_realtime0 = realtime();
|
||||
mm_mapopt_init(&opt);
|
||||
|
||||
while ((c = getopt(argc, argv, "w:k:B:b:t:r:c:f:Vv:NOg:I:d:lRPST:m:L:Dx:H")) >= 0) {
|
||||
while ((c = getopt(argc, argv, "w:k:B:b:t:r:c:f:Vv:NOg:I:d:lRPST:L:Dx:H")) >= 0) {
|
||||
if (c == 'w') w = atoi(optarg);
|
||||
else if (c == 'k') k = atoi(optarg);
|
||||
else if (c == 'b') b = atoi(optarg);
|
||||
|
|
@ -43,7 +43,6 @@ int main(int argc, char *argv[])
|
|||
else if (c == 'd') fnw = optarg; // the above are indexing related options, except -I
|
||||
else if (c == 'r') opt.radius = atoi(optarg);
|
||||
else if (c == 'c') opt.min_cnt = atoi(optarg);
|
||||
else if (c == 'm') opt.merge_frac = atof(optarg);
|
||||
else if (c == 'f') f = atof(optarg);
|
||||
else if (c == 't') n_threads = atoi(optarg);
|
||||
else if (c == 'v') mm_verbose = atoi(optarg);
|
||||
|
|
@ -72,7 +71,6 @@ int main(int argc, char *argv[])
|
|||
if (strcmp(optarg, "ava10k") == 0) {
|
||||
opt.flag |= MM_F_AVA | MM_F_NO_SELF;
|
||||
opt.min_match = 100;
|
||||
opt.merge_frac = 0.0;
|
||||
w = 5;
|
||||
}
|
||||
}
|
||||
|
|
@ -93,7 +91,6 @@ int main(int argc, char *argv[])
|
|||
fprintf(stderr, " Mapping:\n");
|
||||
fprintf(stderr, " -f FLOAT filter out top FLOAT fraction of repetitive minimizers [%.3f]\n", f);
|
||||
fprintf(stderr, " -r INT bandwidth [%d]\n", opt.radius);
|
||||
fprintf(stderr, " -m FLOAT merge two chains if FLOAT fraction of minimizers are shared [%.2f]\n", opt.merge_frac);
|
||||
fprintf(stderr, " -c INT retain a mapping if it consists of >=INT minimizers [%d]\n", opt.min_cnt);
|
||||
fprintf(stderr, " -L INT min matching length [%d]\n", opt.min_match);
|
||||
fprintf(stderr, " -g INT split a mapping if there is a gap longer than INT [%d]\n", opt.max_gap);
|
||||
|
|
@ -129,13 +126,12 @@ int main(int argc, char *argv[])
|
|||
__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), mi->n_seq);
|
||||
if (fpw) {
|
||||
mm_idx_dump(fpw, mi);
|
||||
if (mm_verbose >= 2)
|
||||
if (mm_verbose >= 3)
|
||||
fprintf(stderr, "[M::%s::%.3f*%.2f] dumpped the (partial) index to disk\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0));
|
||||
}
|
||||
/*
|
||||
if (argc != optind + 1) mm_mapopt_update(&opt, mi);
|
||||
for (i = optind + 1; i < argc; ++i)
|
||||
mm_map_file(mi, argv[i], &opt, n_threads, mini_batch_size);
|
||||
*/
|
||||
mm_idx_destroy(mi);
|
||||
}
|
||||
if (fpw) fclose(fpw);
|
||||
|
|
|
|||
215
map.c
215
map.c
|
|
@ -1,25 +1,49 @@
|
|||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include "kthread.h"
|
||||
#include "kvec.h"
|
||||
#include "kalloc.h"
|
||||
#include "sdust.h"
|
||||
#include "minimap.h"
|
||||
#include "bseq.h"
|
||||
|
||||
void mm_mapopt_init(mm_mapopt_t *opt)
|
||||
{
|
||||
opt->n_frag_mini = 100;
|
||||
opt->max_occ_frac = 1e-5f;
|
||||
opt->mid_occ_frac = 1e-3f;
|
||||
opt->sdust_thres = 0;
|
||||
|
||||
opt->radius = 500;
|
||||
opt->max_gap = 10000;
|
||||
opt->min_cnt = 4;
|
||||
opt->min_match = 40;
|
||||
opt->sdust_thres = 0;
|
||||
opt->flag = MM_F_WITH_REP;
|
||||
opt->merge_frac = .5;
|
||||
}
|
||||
|
||||
void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
|
||||
{
|
||||
opt->max_occ = mm_idx_cal_max_occ(mi, opt->max_occ_frac);
|
||||
opt->mid_occ = mm_idx_cal_max_occ(mi, opt->mid_occ_frac);
|
||||
if (mm_verbose >= 3)
|
||||
fprintf(stderr, "[M::%s::%.3f*%.2f] mid_occ = %d; max_occ = %d\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0),
|
||||
opt->mid_occ, opt->max_occ);
|
||||
}
|
||||
|
||||
typedef struct {
|
||||
uint32_t n, is_alloc;
|
||||
uint32_t qpos, span;
|
||||
union {
|
||||
const uint64_t *cr;
|
||||
uint64_t *r;
|
||||
} x;
|
||||
} mm_match_t;
|
||||
|
||||
struct mm_tbuf_s {
|
||||
sdust_buf_t *sdb;
|
||||
mm128_v mini;
|
||||
kvec_t(mm_reg1_t) reg;
|
||||
void *km;
|
||||
void *km, *km_fixed;
|
||||
};
|
||||
|
||||
mm_tbuf_t *mm_tbuf_init(void)
|
||||
|
|
@ -27,6 +51,7 @@ mm_tbuf_t *mm_tbuf_init(void)
|
|||
mm_tbuf_t *b;
|
||||
b = (mm_tbuf_t*)calloc(1, sizeof(mm_tbuf_t));
|
||||
b->km = km_init();
|
||||
b->km_fixed = km_init();
|
||||
b->sdb = sdust_buf_init(b->km);
|
||||
return b;
|
||||
}
|
||||
|
|
@ -34,36 +59,178 @@ mm_tbuf_t *mm_tbuf_init(void)
|
|||
void mm_tbuf_destroy(mm_tbuf_t *b)
|
||||
{
|
||||
if (b == 0) return;
|
||||
km_destroy(b->km_fixed);
|
||||
km_destroy(b->km);
|
||||
free(b);
|
||||
}
|
||||
|
||||
const mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *name)
|
||||
static void mm_dust_minier(mm128_v *mini, int l_seq, const char *seq, int sdust_thres, sdust_buf_t *sdb)
|
||||
{
|
||||
int j;
|
||||
int n_dreg, j, k, u = 0;
|
||||
const uint64_t *dreg;
|
||||
if (sdust_thres <= 0 || sdb == 0) return;
|
||||
dreg = sdust_core((const uint8_t*)seq, l_seq, sdust_thres, 64, &n_dreg, sdb);
|
||||
for (j = k = 0; j < mini->n; ++j) { // squeeze out minimizers that significantly overlap with LCRs
|
||||
int32_t qpos = (uint32_t)mini->a[j].y>>1, span = mini->a[j].x&0xff;
|
||||
int32_t s = qpos - (span - 1), e = s + span;
|
||||
while (u < n_dreg && (uint32_t)dreg[u] <= s) ++u;
|
||||
if (u < n_dreg && dreg[u]>>32 < e) {
|
||||
int v, l = 0;
|
||||
for (v = u; v < n_dreg && dreg[v]>>32 < e; ++v) { // iterate over LCRs overlapping this minimizer
|
||||
int ss = s > dreg[v]>>32? s : dreg[v]>>32;
|
||||
int ee = e < (uint32_t)dreg[v]? e : (uint32_t)dreg[v];
|
||||
l += ee - ss;
|
||||
}
|
||||
if (l <= span>>1) mini->a[k++] = mini->a[j]; // keep the minimizer if less than half of it falls in masked region
|
||||
}
|
||||
}
|
||||
mini->n = k;
|
||||
}
|
||||
|
||||
b->mini.n = 0;
|
||||
mm_sketch(b->km, seq, l_seq, mi->w, mi->k, 0, mi->is_hpc, &b->mini);
|
||||
if (opt->sdust_thres > 0) { // squeeze out minimizers that significantly overlap with LCRs
|
||||
int n_dreg, k, u = 0;
|
||||
const uint64_t *dreg;
|
||||
dreg = sdust_core((const uint8_t*)seq, l_seq, opt->sdust_thres, 64, &n_dreg, b->sdb);
|
||||
for (j = k = 0; j < b->mini.n; ++j) {
|
||||
int32_t qpos = (uint32_t)b->mini.a[j].y>>1, span = b->mini.a[j].x&0xff;
|
||||
int32_t s = qpos - (span - 1), e = s + span;
|
||||
while (u < n_dreg && (uint32_t)dreg[u] <= s) ++u;
|
||||
if (u < n_dreg && dreg[u]>>32 < e) {
|
||||
int v, l = 0;
|
||||
for (v = u; v < n_dreg && dreg[v]>>32 < e; ++v) { // iterate over LCRs overlapping this minimizer
|
||||
int ss = s > dreg[v]>>32? s : dreg[v]>>32;
|
||||
int ee = e < (uint32_t)dreg[v]? e : (uint32_t)dreg[v];
|
||||
l += ee - ss;
|
||||
}
|
||||
if (l <= mi->k>>1) b->mini.a[k++] = b->mini.a[j];
|
||||
void mm_pair_thin(mm_tbuf_t *b, mm_match_t *_m1, mm_match_t *_m2)
|
||||
{
|
||||
}
|
||||
|
||||
void mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, uint32_t m_st, uint32_t m_en)
|
||||
{
|
||||
int i, n = m_en - m_st, last = -1, last2 = -1;
|
||||
mm_match_t *m;
|
||||
|
||||
// convert to local representation
|
||||
m = (mm_match_t*)kmalloc(b->km_fixed, (m_en - m_st) * sizeof(mm_match_t));
|
||||
for (i = 0; i < n; ++i) {
|
||||
int t;
|
||||
mm128_t *p = &b->mini.a[i + m_st];
|
||||
m[i].is_alloc = 0;
|
||||
m[i].qpos = (uint32_t)p->y;
|
||||
m[i].span = p->x & 0xff;
|
||||
m[i].x.cr = mm_idx_get(mi, p->x, &t);
|
||||
m[i].n = t;
|
||||
}
|
||||
|
||||
// pair k-mer thinning
|
||||
for (i = 0; i < n; ++i) {
|
||||
if (m[i].n >= opt->mid_occ && m[i].n < opt->max_occ) {
|
||||
if (last2 < 0) last2 = i;
|
||||
if (last < 0 || m[last].n < m[i].n) last = i;
|
||||
if (last >= 0 && m[last].span + (m[last].qpos>>1) <= m[i].qpos>>1) {
|
||||
mm_pair_thin(b, &m[last], &m[i]);
|
||||
last2 = last = -1;
|
||||
} else if (last2 >= 0 && m[last].span + (m[last].qpos>>1) <= m[i].qpos>>1) {
|
||||
mm_pair_thin(b, &m[last2], &m[i]);
|
||||
last2 = last = -1;
|
||||
}
|
||||
}
|
||||
b->mini.n = k;
|
||||
}
|
||||
kfree(b->km_fixed, m);
|
||||
}
|
||||
|
||||
const mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *name)
|
||||
{
|
||||
uint32_t proc_mini = 0;
|
||||
b->mini.n = 0;
|
||||
mm_sketch(b->km, seq, l_seq, mi->w, mi->k, 0, mi->is_hpc, &b->mini);
|
||||
if (opt->sdust_thres > 0)
|
||||
mm_dust_minier(&b->mini, l_seq, seq, opt->sdust_thres, b->sdb);
|
||||
while (proc_mini < b->mini.n) {
|
||||
uint32_t n = b->mini.n - proc_mini < opt->n_frag_mini * 1.5f? b->mini.n - proc_mini : opt->n_frag_mini;
|
||||
mm_map_frag(opt, mi, b, proc_mini, proc_mini + n);
|
||||
proc_mini += n;
|
||||
}
|
||||
*n_regs = b->reg.n;
|
||||
return b->reg.a;
|
||||
}
|
||||
|
||||
/**************************
|
||||
* Multi-threaded mapping *
|
||||
**************************/
|
||||
|
||||
typedef struct {
|
||||
int mini_batch_size, n_processed, n_threads;
|
||||
const mm_mapopt_t *opt;
|
||||
bseq_file_t *fp;
|
||||
const mm_idx_t *mi;
|
||||
} pipeline_t;
|
||||
|
||||
typedef struct {
|
||||
const pipeline_t *p;
|
||||
int n_seq;
|
||||
bseq1_t *seq;
|
||||
int *n_reg;
|
||||
mm_reg1_t **reg;
|
||||
mm_tbuf_t **buf;
|
||||
} step_t;
|
||||
|
||||
static void worker_for(void *_data, long i, int tid) // kt_for() callback
|
||||
{
|
||||
step_t *step = (step_t*)_data;
|
||||
const mm_reg1_t *regs;
|
||||
int n_regs;
|
||||
|
||||
regs = mm_map(step->p->mi, step->seq[i].l_seq, step->seq[i].seq, &n_regs, step->buf[tid], step->p->opt, step->seq[i].name);
|
||||
step->n_reg[i] = n_regs;
|
||||
if (n_regs > 0) {
|
||||
step->reg[i] = (mm_reg1_t*)malloc(n_regs * sizeof(mm_reg1_t));
|
||||
memcpy(step->reg[i], regs, n_regs * sizeof(mm_reg1_t));
|
||||
}
|
||||
}
|
||||
|
||||
static void *worker_pipeline(void *shared, int step, void *in)
|
||||
{
|
||||
int i, j;
|
||||
pipeline_t *p = (pipeline_t*)shared;
|
||||
if (step == 0) { // step 0: read sequences
|
||||
step_t *s;
|
||||
s = (step_t*)calloc(1, sizeof(step_t));
|
||||
s->seq = bseq_read(p->fp, p->mini_batch_size, &s->n_seq);
|
||||
if (s->seq) {
|
||||
s->p = p;
|
||||
for (i = 0; i < s->n_seq; ++i)
|
||||
s->seq[i].rid = p->n_processed++;
|
||||
s->buf = (mm_tbuf_t**)calloc(p->n_threads, sizeof(mm_tbuf_t*));
|
||||
for (i = 0; i < p->n_threads; ++i)
|
||||
s->buf[i] = mm_tbuf_init();
|
||||
s->n_reg = (int*)calloc(s->n_seq, sizeof(int));
|
||||
s->reg = (mm_reg1_t**)calloc(s->n_seq, sizeof(mm_reg1_t*));
|
||||
return s;
|
||||
} else free(s);
|
||||
} else if (step == 1) { // step 1: map
|
||||
kt_for(p->n_threads, worker_for, in, ((step_t*)in)->n_seq);
|
||||
return in;
|
||||
} else if (step == 2) { // step 2: output
|
||||
step_t *s = (step_t*)in;
|
||||
const mm_idx_t *mi = p->mi;
|
||||
for (i = 0; i < p->n_threads; ++i) mm_tbuf_destroy(s->buf[i]);
|
||||
free(s->buf);
|
||||
for (i = 0; i < s->n_seq; ++i) {
|
||||
bseq1_t *t = &s->seq[i];
|
||||
for (j = 0; j < s->n_reg[i]; ++j) {
|
||||
mm_reg1_t *r = &s->reg[i][j];
|
||||
if (r->len < p->opt->min_match) continue;
|
||||
printf("%s\t%d\t%d\t%d\t%c\t", t->name, t->l_seq, r->qs, r->qe, "+-"[r->rev]);
|
||||
if (mi->seq[r->rid].name) fputs(mi->seq[r->rid].name, stdout);
|
||||
else printf("%d", r->rid + 1);
|
||||
printf("\t%d\t%d\t%d\t%d\t%d\t255\tcm:i:%d\n", mi->seq[r->rid].len, r->rs, r->re, r->len,
|
||||
r->re - r->rs > r->qe - r->qs? r->re - r->rs : r->qe - r->qs, r->cnt);
|
||||
}
|
||||
free(s->reg[i]);
|
||||
free(s->seq[i].seq); free(s->seq[i].name);
|
||||
}
|
||||
free(s->reg); free(s->n_reg); free(s->seq);
|
||||
free(s);
|
||||
}
|
||||
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)
|
||||
{
|
||||
pipeline_t pl;
|
||||
memset(&pl, 0, sizeof(pipeline_t));
|
||||
pl.fp = bseq_open(fn);
|
||||
if (pl.fp == 0) return -1;
|
||||
pl.opt = opt, pl.mi = idx;
|
||||
pl.n_threads = n_threads, pl.mini_batch_size = mini_batch_size;
|
||||
kt_pipeline(n_threads == 1? 1 : 2, worker_pipeline, &pl, 3);
|
||||
bseq_close(pl.fp);
|
||||
return 0;
|
||||
}
|
||||
|
|
|
|||
14
minimap.h
14
minimap.h
|
|
@ -50,13 +50,18 @@ typedef struct {
|
|||
} mm_reg1_t;
|
||||
|
||||
typedef struct {
|
||||
int n_frag_mini;
|
||||
float max_occ_frac;
|
||||
float mid_occ_frac;
|
||||
int sdust_thres; // score threshold for SDUST; 0 to disable
|
||||
int flag; // see MM_F_* macros
|
||||
int radius; // bandwidth to cluster hits
|
||||
int max_gap; // break a chain if there are no minimizers in a max_gap window
|
||||
int min_cnt; // minimum number of minimizers to start a chain
|
||||
int min_match;
|
||||
int sdust_thres; // score threshold for SDUST; 0 to disable
|
||||
int flag; // see MM_F_* macros
|
||||
float merge_frac; // merge two chains if merge_frac fraction of minimzers are shared between the chains
|
||||
|
||||
int max_occ;
|
||||
int mid_occ;
|
||||
} mm_mapopt_t;
|
||||
|
||||
extern int mm_verbose;
|
||||
|
|
@ -81,7 +86,7 @@ void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, i
|
|||
mm_idx_t *mm_idx_init(int w, int k, int b, int is_hpc);
|
||||
void mm_idx_destroy(mm_idx_t *mi);
|
||||
mm_idx_t *mm_idx_gen(struct bseq_file_s *fp, int w, int k, int b, int is_hpc, int mini_batch_size, int n_threads, uint64_t batch_size, int keep_name);
|
||||
void mm_idx_set_max_occ(mm_idx_t *mi, float f);
|
||||
uint32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f);
|
||||
const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n);
|
||||
|
||||
mm_idx_t *mm_idx_build(const char *fn, int w, int k, int is_hpc, int n_threads);
|
||||
|
|
@ -92,6 +97,7 @@ mm_idx_t *mm_idx_load(FILE *fp);
|
|||
|
||||
// mapping
|
||||
void mm_mapopt_init(mm_mapopt_t *opt);
|
||||
void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi);
|
||||
mm_tbuf_t *mm_tbuf_init(void);
|
||||
void mm_tbuf_destroy(mm_tbuf_t *b);
|
||||
const mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *name);
|
||||
|
|
|
|||
Loading…
Reference in New Issue