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write hits to tmp files (unfinished)

This commit is contained in:
Heng Li 2018-07-14 12:15:10 -04:00
parent 5cfa621b2d
commit 1a55227d5a
8 changed files with 103 additions and 31 deletions
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2
Makefile
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@ -1,7 +1,7 @@
CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra
CPPFLAGS= -DHAVE_KALLOC
INCLUDES=
OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o ksw2_ll_sse.o
OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o
PROG= minimap2
PROG_EXTRA= sdust minimap2-lite
LIBS= -lm -lz -lpthread

2
index.c
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@ -563,7 +563,7 @@ mm_idx_t *mm_idx_reader_read(mm_idx_reader_t *r, int n_threads)
mi = mm_idx_gen(r->fp.seq, r->opt.w, r->opt.k, r->opt.bucket_bits, r->opt.flag, r->opt.mini_batch_size, n_threads, r->opt.batch_size);
if (mi) {
if (r->fp_out) mm_idx_dump(r->fp_out, mi);
++r->n_parts;
mi->index = r->n_parts++;
}
return mi;
}

2
main.c
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@ -61,6 +61,7 @@ static struct option long_options[] = {
{ "score-N", required_argument, 0, 0 }, // 31
{ "eqx", no_argument, 0, 0 }, // 32
{ "paf-no-hit", no_argument, 0, 0 }, // 33
{ "split-prefix", required_argument, 0, 0 }, // 34
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@ -181,6 +182,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==31) opt.sc_ambi = atoi(optarg); // --score-N
else if (c == 0 && long_idx ==32) opt.flag |= MM_F_EQX; // --eqx
else if (c == 0 && long_idx ==33) opt.flag |= MM_F_PAF_NO_HIT; // --paf-no-hit
else if (c == 0 && long_idx ==34) opt.split_prefix = optarg; // --split-prefix
else if (c == 0 && long_idx == 14) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, long_idx, optarg, 1);
} else if (c == 0 && long_idx == 15) { // --secondary

73
map.c
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@ -262,7 +262,7 @@ static mm_reg1_t *align_regs(const mm_mapopt_t *opt, const mm_idx_t *mi, void *k
return regs;
}
void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
int mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
{
int i, j, rep_len, qlen_sum, n_regs0, n_mini_pos;
int max_chain_gap_qry, max_chain_gap_ref, is_splice = !!(opt->flag & MM_F_SPLICE), is_sr = !!(opt->flag & MM_F_SR);
@ -277,7 +277,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
for (i = 0, qlen_sum = 0; i < n_segs; ++i)
qlen_sum += qlens[i], n_regs[i] = 0, regs[i] = 0;
if (qlen_sum == 0 || n_segs <= 0 || n_segs > MM_MAX_SEG) return;
if (qlen_sum == 0 || n_segs <= 0 || n_segs > MM_MAX_SEG) return 0;
hash = qname? __ac_X31_hash_string(qname) : 0;
hash ^= __ac_Wang_hash(qlen_sum) + __ac_Wang_hash(opt->seed);
@ -375,6 +375,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
b->km = km_init();
}
}
return rep_len;
}
mm_reg1_t *mm_map(const mm_idx_t *mi, int qlen, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
@ -394,13 +395,14 @@ typedef struct {
mm_bseq_file_t **fp;
const mm_idx_t *mi;
kstring_t str;
FILE *fp_split;
} pipeline_t;
typedef struct {
const pipeline_t *p;
int n_seq, n_frag;
mm_bseq1_t *seq;
int *n_reg, *seg_off, *n_seg;
int *n_reg, *seg_off, *n_seg, *rep_len;
mm_reg1_t **reg;
mm_tbuf_t **buf;
} step_t;
@ -422,9 +424,12 @@ static void worker_for(void *_data, long i, int tid) // kt_for() callback
}
if (s->p->opt->flag & MM_F_INDEPEND_SEG) {
for (j = 0; j < s->n_seg[i]; ++j)
mm_map_frag(s->p->mi, 1, &qlens[j], &qseqs[j], &s->n_reg[off+j], &s->reg[off+j], b, s->p->opt, s->seq[off+j].name);
s->rep_len[off + j] = mm_map_frag(s->p->mi, 1, &qlens[j], &qseqs[j], &s->n_reg[off+j], &s->reg[off+j], b, s->p->opt, s->seq[off+j].name);
} else {
mm_map_frag(s->p->mi, s->n_seg[i], qlens, qseqs, &s->n_reg[off], &s->reg[off], b, s->p->opt, s->seq[off].name);
int rep_len;
rep_len = mm_map_frag(s->p->mi, s->n_seg[i], qlens, qseqs, &s->n_reg[off], &s->reg[off], b, s->p->opt, s->seq[off].name);
for (j = 0; j < s->n_seg[i]; ++j)
s->rep_len[off + j] = rep_len;
}
for (j = 0; j < s->n_seg[i]; ++j) // flip the query strand and coordinate to the original read strand
if (s->n_seg[i] == 2 && ((j == 0 && (pe_ori>>1&1)) || (j == 1 && (pe_ori&1)))) {
@ -459,9 +464,10 @@ static void *worker_pipeline(void *shared, int step, void *in)
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(3 * s->n_seq, sizeof(int));
s->seg_off = s->n_reg + s->n_seq; // seg_off and n_seg are allocated together with n_reg
s->n_reg = (int*)calloc(4 * s->n_seq, sizeof(int));
s->seg_off = s->n_reg + s->n_seq; // seg_off, n_seg and rep_len are allocated together with n_reg
s->n_seg = s->seg_off + s->n_seq;
s->rep_len = s->n_seg + s->n_seq;
s->reg = (mm_reg1_t**)calloc(s->n_seq, sizeof(mm_reg1_t*));
for (i = 1, j = 0; i <= s->n_seq; ++i)
if (i == s->n_seq || !frag_mode || !mm_qname_same(s->seq[i-1].name, s->seq[i].name)) {
@ -485,28 +491,35 @@ static void *worker_pipeline(void *shared, int step, void *in)
int seg_st = s->seg_off[k], seg_en = s->seg_off[k] + s->n_seg[k];
for (i = seg_st; i < seg_en; ++i) {
mm_bseq1_t *t = &s->seq[i];
for (j = 0; j < s->n_reg[i]; ++j) {
mm_reg1_t *r = &s->reg[i][j];
assert(!r->sam_pri || r->id == r->parent);
if ((p->opt->flag & MM_F_NO_PRINT_2ND) && r->id != r->parent)
continue;
if (p->opt->flag & MM_F_OUT_SAM)
mm_write_sam2(&p->str, mi, t, i - seg_st, j, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag);
else
mm_write_paf(&p->str, mi, t, r, km, p->opt->flag);
mm_err_puts(p->str.s);
if (p->opt->split_prefix) {
mm_err_fwrite(&s->n_reg[i], sizeof(s->n_reg[i]), 1, p->fp_split);
mm_err_fwrite(&s->rep_len[i], sizeof(s->rep_len[i]), 1, p->fp_split);
}
if (s->n_reg[i] == 0) {
if (p->opt->flag & MM_F_OUT_SAM) {
mm_write_sam2(&p->str, mi, t, i - seg_st, -1, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag);
mm_err_puts(p->str.s);
} else if (p->opt->flag & MM_F_PAF_NO_HIT) {
mm_write_paf(&p->str, mi, t, 0, 0, p->opt->flag);
mm_err_puts(p->str.s);
if (s->n_reg[i] > 0) {
for (j = 0; j < s->n_reg[i]; ++j) {
mm_reg1_t *r = &s->reg[i][j];
assert(!r->sam_pri || r->id == r->parent);
if ((p->opt->flag & MM_F_NO_PRINT_2ND) && r->id != r->parent)
continue;
if (p->opt->split_prefix) {
mm_err_fwrite(r, sizeof(mm_reg1_t), 1, p->fp_split);
if (p->opt->flag & MM_F_CIGAR) {
mm_err_fwrite(&r->p->capacity, 4, 1, p->fp_split);
mm_err_fwrite(r->p, r->p->capacity, 4, p->fp_split);
}
} else {
if (p->opt->flag & MM_F_OUT_SAM)
mm_write_sam2(&p->str, mi, t, i - seg_st, j, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag);
else
mm_write_paf(&p->str, mi, t, r, km, p->opt->flag);
mm_err_puts(p->str.s);
}
}
}
if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) { // write an unmapped record
mm_write_sam2(&p->str, mi, t, i - seg_st, -1, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag);
} else if (p->opt->flag & (MM_F_OUT_SAM|MM_F_PAF_NO_HIT)) {
if (p->opt->flag & MM_F_OUT_SAM)
mm_write_sam2(&p->str, mi, t, i - seg_st, -1, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag);
else
mm_write_paf(&p->str, mi, t, 0, 0, p->opt->flag);
mm_err_puts(p->str.s);
}
}
@ -517,7 +530,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
if (s->seq[i].qual) free(s->seq[i].qual);
}
}
free(s->reg); free(s->n_reg); free(s->seq); // seg_off and n_seg were allocated with reg; no memory leak here
free(s->reg); free(s->n_reg); free(s->seq); // seg_off, n_seg and rep_len were allocated with reg; no memory leak here
km_destroy(km);
if (mm_verbose >= 3)
fprintf(stderr, "[M::%s::%.3f*%.2f] mapped %d sequences\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), s->n_seq);
@ -548,9 +561,13 @@ int mm_map_file_frag(const mm_idx_t *idx, int n_segs, const char **fn, const mm_
pl.opt = opt, pl.mi = idx;
pl.n_threads = n_threads > 1? n_threads : 1;
pl.mini_batch_size = opt->mini_batch_size;
if (opt->split_prefix)
pl.fp_split = mm_split_init(opt->split_prefix, idx);
pl_threads = n_threads == 1? 1 : (opt->flag&MM_F_2_IO_THREADS)? 3 : 2;
kt_pipeline(pl_threads, worker_pipeline, &pl, 3);
free(pl.str.s);
if (opt->split_prefix)
fclose(pl.fp_split);
for (i = 0; i < n_segs; ++i)
mm_bseq_close(pl.fp[i]);
free(pl.fp);

5
minimap.h
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@ -60,6 +60,7 @@ typedef struct {
typedef struct {
int32_t b, w, k, flag;
uint32_t n_seq; // number of reference sequences
int32_t index;
mm_idx_seq_t *seq; // sequence name, length and offset
uint32_t *S; // 4-bit packed sequence
struct mm_idx_bucket_s *B; // index (hidden)
@ -136,6 +137,8 @@ typedef struct {
int32_t mid_occ; // ignore seeds with occurrences above this threshold
int32_t max_occ;
int mini_batch_size; // size of a batch of query bases to process in parallel
const char *split_prefix;
} mm_mapopt_t;
// index reader
@ -318,7 +321,7 @@ void mm_tbuf_destroy(mm_tbuf_t *b);
*/
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);
void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname);
int mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname);
/**
* Align a fasta/fastq file and print alignments to stdout

20
misc.c
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@ -131,6 +131,26 @@ void mm_err_puts(const char *str)
}
}
void mm_err_fwrite(const void *p, size_t size, size_t nitems, FILE *fp)
{
int ret;
ret = fwrite(p, size, nitems, fp);
if (ret == EOF) {
fprintf(stderr, "[ERROR] failed to write data\n");
exit(EXIT_FAILURE);
}
}
void mm_err_fread(void *p, size_t size, size_t nitems, FILE *fp)
{
int ret;
ret = fread(p, size, nitems, fp);
if (ret == EOF) {
fprintf(stderr, "[ERROR] failed to read data\n");
exit(EXIT_FAILURE);
}
}
#include "ksort.h"
#define sort_key_128x(a) ((a).x)

4
mmpriv.h
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@ -86,7 +86,11 @@ mm_seg_t *mm_seg_gen(void *km, uint32_t hash, int n_segs, const int *qlens, int
void mm_seg_free(void *km, int n_segs, mm_seg_t *segs);
void mm_pair(void *km, int max_gap_ref, int dp_bonus, int sub_diff, int match_sc, const int *qlens, int *n_regs, mm_reg1_t **regs);
FILE *mm_split_init(const char *prefix, const mm_idx_t *mi);
void mm_err_puts(const char *str);
void mm_err_fwrite(const void *p, size_t size, size_t nitems, FILE *fp);
void mm_err_fread(void *p, size_t size, size_t nitems, FILE *fp);
#ifdef __cplusplus
}

26
splitidx.c 100644
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@ -0,0 +1,26 @@
#include <string.h>
#include <assert.h>
#include <stdlib.h>
#include <stdio.h>
#include "mmpriv.h"
FILE *mm_split_init(const char *prefix, const mm_idx_t *mi)
{
char *fn;
FILE *fp;
uint32_t i;
fn = (char*)calloc(strlen(prefix) + 10, 1);
sprintf(fn, "%s.%.4d.tmp", prefix, mi->index);
fp = fopen(fn, "wb");
assert(fp);
mm_err_fwrite(&mi->n_seq, 4, 1, fp);
for (i = 0; i < mi->n_seq; ++i) {
uint8_t l;
l = strlen(mi->seq[i].name);
mm_err_fwrite(&l, 1, 1, fp);
mm_err_fwrite(mi->seq[i].name, 1, l, fp);
mm_err_fwrite(&mi->seq[i].len, 4, 1, fp);
}
free(fn);
return fp;
}