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fast-bwa/bwashm.c

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C
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#include <sys/types.h>
#include <sys/mman.h>
#include <string.h>
#include <stdlib.h>
#include <limits.h>
#include <unistd.h>
#include <fcntl.h>
#include <errno.h>
#include <stdio.h>
#include "bwa.h"
#include "ertindex.h"
int bwa_shm_stage(bwaidx_t *idx, const char *hint, int useERT)
{
const char *name;
uint8_t *shm, *shm_idx;
uint16_t *cnt;
int shmid, to_init = 0, l;
char path[PATH_MAX + 1], *tmpfn = 0;
if (hint == 0 || hint[0] == 0) return -1;
for (name = hint + strlen(hint) - 1; name >= hint && *name != '/'; --name);
++name;
if ((shmid = shm_open("/bwactl", O_RDWR, 0)) < 0) {
shmid = shm_open("/bwactl", O_CREAT|O_RDWR|O_EXCL, 0644);
to_init = 1;
}
if (shmid < 0) return -1;
if (ftruncate(shmid, BWA_CTL_SIZE) < 0) return -1;
shm = mmap(0, BWA_CTL_SIZE, PROT_READ|PROT_WRITE, MAP_SHARED, shmid, 0);
cnt = (uint16_t*)shm;
if (to_init) {
memset(shm, 0, BWA_CTL_SIZE);
cnt[1] = 4;
}
// 将所有索引数据放在连续的内存空间里
if (idx->mem == 0) {
if (useERT) bwa_ertidx2mem(idx);
else bwa_fmtidx2mem(idx);
}
if (tmpfn) {
FILE *fp;
if ((fp = fopen(tmpfn, "wb")) != 0) {
int64_t rest = idx->l_mem;
while (rest > 0) {
int64_t l = rest < 0x1000000? rest : 0x1000000;
rest -= fwrite(&idx->mem[idx->l_mem - rest], 1, l, fp);
}
fclose(fp);
free(idx->mem); idx->mem = 0;
} else {
fprintf(stderr, "[W::%s] fail to create the temporary file. Option '-f' is ignored.\n", __func__);
tmpfn = 0;
}
}
strcat(strcpy(path, "/bwaidx-"), name);
if ((shmid = shm_open(path, O_CREAT|O_RDWR|O_EXCL, 0644)) < 0) {
shm_unlink(path);
perror("shm_open()");
return -1;
}
l = 8 + strlen(name) + 1;
if (cnt[1] + l > BWA_CTL_SIZE) return -1;
memcpy(shm + cnt[1], &idx->l_mem, 8);
memcpy(shm + cnt[1] + 8, name, l - 8);
cnt[1] += l; ++cnt[0];
if (ftruncate(shmid, idx->l_mem) < 0) return -1;
shm_idx = mmap(0, idx->l_mem, PROT_READ|PROT_WRITE, MAP_SHARED, shmid, 0);
if (tmpfn) {
FILE *fp;
fp = fopen(tmpfn, "rb");
int64_t rest = idx->l_mem;
while (rest > 0) {
int64_t l = rest < 0x1000000? rest : 0x1000000;
rest -= fread(&shm_idx[idx->l_mem - rest], 1, l, fp);
}
fclose(fp);
unlink(tmpfn);
} else {
memcpy(shm_idx, idx->mem, idx->l_mem);
free(idx->mem);
}
if (useERT)
bwa_mem2ertidx(idx->l_mem, shm_idx, idx);
else
bwa_mem2fmtidx(idx->l_mem, shm_idx, idx);
idx->is_shm = 1;
return 0;
}
#define INIT_SHM_LOAD \
const char *name; \
uint8_t *shm, *shm_idx; \
uint16_t *cnt, i; \
char *p, path[PATH_MAX + 1]; \
int shmid; \
int64_t l_mem; \
bwaidx_t *idx; \
if (hint == 0 || hint[0] == 0) return 0; \
for (name = hint + strlen(hint) - 1; name >= hint && *name != '/'; --name); \
++name; \
if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return 0; \
shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0); \
cnt = (uint16_t*)shm; \
if (cnt[0] == 0) return 0; \
for (i = 0, p = (char*)(shm + 4); i < cnt[0]; ++i) { \
memcpy(&l_mem, p, 8); p += 8; \
if (strcmp(p, name) == 0) break; \
p += strlen(p) + 1; \
} \
if (i == cnt[0]) return 0; \
strcat(strcpy(path, "/bwaidx-"), name); \
if ((shmid = shm_open(path, O_RDONLY, 0)) < 0) return 0; \
shm_idx = mmap(0, l_mem, PROT_READ, MAP_SHARED, shmid, 0); \
idx = calloc(1, sizeof(bwaidx_t));
bwaidx_t *bwa_ertidx_load_from_shm(const char *hint_)
{
char hint[PATH_MAX];
char fn[PATH_MAX];
FILE *fp;
sprintf(hint, "%s.ert", hint_);
INIT_SHM_LOAD;
bwa_mem2ertidx(l_mem, shm_idx, idx);
idx->ert->bref = (uint8_t *)malloc(idx->ert->bref_size * sizeof(uint8_t));
sprintf(fn, "%s.ert.0123", hint_);
fp = xopen(fn, "rb");
err_fread_noeof(idx->ert->bref, sizeof(uint8_t), idx->ert->bref_size, fp);
err_fclose(fp);
idx->is_shm = 1;
return idx;
}
bwaidx_t *bwa_fmtidx_load_from_shm(const char *hint)
{
INIT_SHM_LOAD;
bwa_mem2fmtidx(l_mem, shm_idx, idx);
idx->is_shm = 1;
return idx;
}
bwaidx_t *bwa_idx_load_from_shm(const char *hint)
{
const char *name;
uint8_t *shm, *shm_idx;
uint16_t *cnt, i;
char *p, path[PATH_MAX + 1];
int shmid;
int64_t l_mem;
bwaidx_t *idx;
if (hint == 0 || hint[0] == 0) return 0;
for (name = hint + strlen(hint) - 1; name >= hint && *name != '/'; --name);
++name;
if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return 0;
shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0);
cnt = (uint16_t*)shm;
if (cnt[0] == 0) return 0;
for (i = 0, p = (char*)(shm + 4); i < cnt[0]; ++i) {
memcpy(&l_mem, p, 8); p += 8;
if (strcmp(p, name) == 0) break;
p += strlen(p) + 1;
}
if (i == cnt[0]) return 0;
strcat(strcpy(path, "/bwaidx-"), name);
if ((shmid = shm_open(path, O_RDONLY, 0)) < 0) return 0;
shm_idx = mmap(0, l_mem, PROT_READ, MAP_SHARED, shmid, 0);
idx = calloc(1, sizeof(bwaidx_t));
bwa_mem2idx(l_mem, shm_idx, idx);
idx->is_shm = 1;
return idx;
}
int bwa_shm_test(const char *hint)
{
int shmid;
uint16_t *cnt, i;
char *p, *shm;
const char *name;
if (hint == 0 || hint[0] == 0) return 0;
for (name = hint + strlen(hint) - 1; name >= hint && *name != '/'; --name);
++name;
if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return 0;
shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0);
cnt = (uint16_t*)shm;
for (i = 0, p = shm + 4; i < cnt[0]; ++i) {
if (strcmp(p + 8, name) == 0) return 1;
p += strlen(p) + 9;
}
return 0;
}
int bwa_shm_list(void)
{
int shmid;
uint16_t *cnt, i;
char *p, *shm;
if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return -1;
shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0);
cnt = (uint16_t*)shm;
for (i = 0, p = shm + 4; i < cnt[0]; ++i) {
int64_t l_mem;
memcpy(&l_mem, p, 8); p += 8;
printf("%s\t%ld\n", p, (long)l_mem);
p += strlen(p) + 1;
}
return 0;
}
int bwa_shm_destroy(void)
{
int shmid;
uint16_t *cnt, i;
char *p, *shm;
char path[PATH_MAX + 1];
if ((shmid = shm_open("/bwactl", O_RDONLY, 0)) < 0) return -1;
shm = mmap(0, BWA_CTL_SIZE, PROT_READ, MAP_SHARED, shmid, 0);
cnt = (uint16_t*)shm;
for (i = 0, p = shm + 4; i < cnt[0]; ++i) {
int64_t l_mem;
memcpy(&l_mem, p, 8); p += 8;
strcat(strcpy(path, "/bwaidx-"), p);
shm_unlink(path);
p += strlen(p) + 1;
}
munmap(shm, BWA_CTL_SIZE);
shm_unlink("/bwactl");
return 0;
}
int bwa_shm_stage_ert(const char *idx_prefix)
{
const char *name;
uint8_t *shm, *mem;
uint16_t *cnt;
int shmid, to_init = 0, l;
char path[PATH_MAX], ert_prefix[PATH_MAX];
int64_t l_mem = 0, x = 0, k = 0;
char fn[PATH_MAX];
FILE *fp;
ERT ert;
bntseq_t *bns;
int i;
// clac l_mem
// ert
x = sizeof(ERT); l_mem += x;
sprintf(fn, "%s.ert.mlt.table", idx_prefix);
fp = xopen(fn, "rb");
err_fseek(fp, 0L, SEEK_END);
ert.mlt_size = ftell(fp);
err_fclose(fp);
// multi-level tree
x = ert.mlt_size; l_mem += x;
// kmer entry
ert.kmer_size = numKmers * sizeof(uint64_t);
x = ert.kmer_size; l_mem += x;
// binary ref
sprintf(fn, "%s.ert.0123", idx_prefix);
fp = xopen(fn, "rb");
fseek(fp, 0L, SEEK_END);
ert.bref_size = ftell(fp);
// x = ert.bref_size; l_mem += x;
err_fclose(fp);
// bns
x = sizeof(bntseq_t); l_mem += x;
bns = bns_restore(idx_prefix);
x = bns->n_holes * sizeof(bntamb1_t); l_mem += x;
x = bns->n_seqs * sizeof(bntann1_t); l_mem += x;
for (i = 0; i < bns->n_seqs; ++i) {
x = strlen(bns->anns[i].name) + 1; l_mem += x;
x = strlen(bns->anns[i].anno) + 1; l_mem += x;
}
// pac
x = bns->l_pac / 4 + 1; l_mem += x;
fprintf(stderr, "l_mem: %ld\n", l_mem);
sprintf(ert_prefix, "%s.ert", idx_prefix);
for (name = ert_prefix + strlen(ert_prefix) - 1; name >= ert_prefix && *name != '/'; --name);
++name;
if ((shmid = shm_open("/bwactl", O_RDWR, 0)) < 0) {
shmid = shm_open("/bwactl", O_CREAT|O_RDWR|O_EXCL, 0644);
to_init = 1;
}
if (shmid < 0) return -1;
if (ftruncate(shmid, BWA_CTL_SIZE) < 0) return -1;
shm = mmap(0, BWA_CTL_SIZE, PROT_READ|PROT_WRITE, MAP_SHARED, shmid, 0);
cnt = (uint16_t*)shm;
if (to_init) {
memset(shm, 0, BWA_CTL_SIZE);
cnt[1] = 4;
}
strcat(strcpy(path, "/bwaidx-"), name);
if ((shmid = shm_open(path, O_CREAT|O_RDWR|O_EXCL, 0644)) < 0) {
shm_unlink(path);
perror("shm_open()");
return -1;
}
l = 8 + strlen(name) + 1;
if (cnt[1] + l > BWA_CTL_SIZE) return -1;
memcpy(shm + cnt[1], &l_mem, 8);
memcpy(shm + cnt[1] + 8, name, l - 8);
cnt[1] += l; ++cnt[0];
if (ftruncate(shmid, l_mem) < 0) return -1;
mem = mmap(0, l_mem, PROT_READ|PROT_WRITE, MAP_SHARED, shmid, 0);
// write to share mem
// ert
x = sizeof(ERT);
memcpy(mem, &ert, x); k = x;
// multi-level tree
sprintf(fn, "%s.ert.mlt.table", idx_prefix);
fp = xopen(fn, "rb");
x = ert.mlt_size;
fread_fix(fp, x, mem + k); k += x;
err_fclose(fp);
// kmer entry
sprintf(fn, "%s.ert.kmer.table", idx_prefix);
fp = xopen(fn, "rb");
x = ert.kmer_size;
fread_fix(fp, x, mem + k); k += x;
err_fclose(fp);
// binary ref
// sprintf(fn, "%s.ert.0123", idx_prefix);
// fp = xopen(fn, "rb");
// x = ert.bref_size;
// fread_fix(fp, x, mem + k); k += x;
// err_fclose(fp);
// bns
x = sizeof(bntseq_t); memcpy(mem + k, bns, x); k += x;
x = bns->n_holes * sizeof(bntamb1_t); memcpy(mem + k, bns->ambs, x); k += x;
x = bns->n_seqs * sizeof(bntann1_t); memcpy(mem + k, bns->anns, x); k += x;
for (i = 0; i < bns->n_seqs; ++i) {
x = strlen(bns->anns[i].name) + 1; memcpy(mem + k, bns->anns[i].name, x); k += x;
x = strlen(bns->anns[i].anno) + 1; memcpy(mem + k, bns->anns[i].anno, x); k += x;
}
// pac
x = bns->l_pac / 4 + 1;
err_fread_noeof(mem + k, 1, x, bns->fp_pac); k += x;// concatenated 2-bit encoded sequence
err_fclose(bns->fp_pac);
fprintf(stderr, "k: %ld\n", k);
return 0;
}
int bwa_shm_stage_fmt(const char *idx_prefix)
{
const char *name;
uint8_t *shm, *mem;
uint16_t *cnt;
int shmid, to_init = 0, l;
char path[PATH_MAX];
int64_t l_mem = 0, x = 0, k = 0;
char fn[PATH_MAX];
FILE *fp;
FMTIndex fmt;
bntseq_t *bns;
int i;
// clac l_mem
// fmt
x = sizeof(FMTIndex); l_mem += x;
sprintf(fn, "%s.fmt", idx_prefix);
fp = xopen(fn, "rb");
err_fseek(fp, 0, SEEK_END);
x = ftell(fp) - sizeof(bwtint_t) * 6 - 3; l_mem += x;
fmt.bwt_size = x >> 2;
fseek(fp, 0, SEEK_SET);
err_fread_noeof(&fmt.primary, sizeof(bwtint_t), 1, fp);
err_fread_noeof(&fmt.sec_primary, sizeof(bwtint_t), 1, fp);
err_fread_noeof(&fmt.sec_bcp, sizeof(uint8_t), 1, fp);
err_fread_noeof(&fmt.first_base, sizeof(uint8_t), 1, fp);
err_fread_noeof(&fmt.last_base, sizeof(uint8_t), 1, fp);
err_fread_noeof(fmt.L2 + 1, sizeof(bwtint_t), 4, fp);
fmt.seq_len = fmt.L2[4];
fmt_gen_cnt_occ(&fmt);
err_fclose(fp);
// sa
sprintf(fn, "%s.bytesa", idx_prefix);
fp = xopen(fn, "rb");
err_fseek(fp, sizeof(bwtint_t) * 5, SEEK_SET);
err_fread_noeof(&fmt.sa_intv, sizeof(bwtint_t), 1, fp);
fmt.n_sa = (fmt.seq_len + fmt.sa_intv) / fmt.sa_intv;
x = SA_BYTES(fmt.n_sa); l_mem += x;
err_fclose(fp);
// kmaer hash
x = (1 << (10 << 1)) * sizeof(KmerEntryArr)
+ (1 << (11 << 1)) * sizeof(KmerEntry)
+ (1 << (12 << 1)) * sizeof(KmerEntry);
#if HASH_KMER_LEN > 12
x += (1 << (13 << 1)) * sizeof(KmerEntry);
#endif
#if HASH_KMER_LEN > 13
x += (1 << (14 << 1)) * sizeof(KmerEntry);
#endif
l_mem += x;
// bns
x = sizeof(bntseq_t); l_mem += x;
bns = bns_restore(idx_prefix);
x = bns->n_holes * sizeof(bntamb1_t); l_mem += x;
x = bns->n_seqs * sizeof(bntann1_t); l_mem += x;
for (i = 0; i < bns->n_seqs; ++i) {
x = strlen(bns->anns[i].name) + 1; l_mem += x;
x = strlen(bns->anns[i].anno) + 1; l_mem += x;
}
// pac
x = bns->l_pac / 4 + 1; l_mem += x;
fmt.l_pac = bns->l_pac;
fprintf(stderr, "l_mem: %ld\n", l_mem);
for (name = idx_prefix + strlen(idx_prefix) - 1; name >= idx_prefix && *name != '/'; --name) ;
++name;
if ((shmid = shm_open("/bwactl", O_RDWR, 0)) < 0) {
shmid = shm_open("/bwactl", O_CREAT|O_RDWR|O_EXCL, 0644);
to_init = 1;
}
if (shmid < 0) return -1;
if (ftruncate(shmid, BWA_CTL_SIZE) < 0) return -1;
shm = mmap(0, BWA_CTL_SIZE, PROT_READ|PROT_WRITE, MAP_SHARED, shmid, 0);
cnt = (uint16_t*)shm;
if (to_init) {
memset(shm, 0, BWA_CTL_SIZE);
cnt[1] = 4;
}
strcat(strcpy(path, "/bwaidx-"), name);
if ((shmid = shm_open(path, O_CREAT|O_RDWR|O_EXCL, 0644)) < 0) {
shm_unlink(path);
perror("shm_open()");
return -1;
}
l = 8 + strlen(name) + 1;
if (cnt[1] + l > BWA_CTL_SIZE) return -1;
memcpy(shm + cnt[1], &l_mem, 8);
memcpy(shm + cnt[1] + 8, name, l - 8);
cnt[1] += l; ++cnt[0];
if (ftruncate(shmid, l_mem) < 0) return -1;
mem = mmap(0, l_mem, PROT_READ|PROT_WRITE, MAP_SHARED, shmid, 0);
// write to share mem
// fmt
x = sizeof(FMTIndex);
memcpy(mem, &fmt, x); k = x;
sprintf(fn, "%s.fmt", idx_prefix);
fp = xopen(fn, "rb");
err_fseek(fp, sizeof(bwtint_t) * 6 + 3, SEEK_SET);
x = fmt.bwt_size * 4;
fread_fix(fp, x, mem + k); k += x;
err_fclose(fp);
// sa
sprintf(fn, "%s.bytesa", idx_prefix);
fp = xopen(fn, "rb");
err_fseek(fp, sizeof(bwtint_t) * 7, SEEK_SET);
x = SA_BYTES(fmt.n_sa);
fread_fix(fp, x, mem + k); k += x;
err_fclose(fp);
// kmer hash
sprintf(fn, "%s.kmer", idx_prefix);
fp = xopen(fn, "rb");
x = (1 << (10 << 1)) * sizeof(KmerEntryArr);
fread_fix(fp, x, mem + k); k += x;
x = (1 << (11 << 1)) * sizeof(KmerEntry);
fread_fix(fp, x, mem + k); k += x;
x = (1 << (12 << 1)) * sizeof(KmerEntry);
fread_fix(fp, x, mem + k); k += x;
#if HASH_KMER_LEN > 12
x = (1 << (13 << 1)) * sizeof(KmerEntry);
fread_fix(fp, x, mem + k); k += x;
#endif
#if HASH_KMER_LEN > 13
x = (1 << (14 << 1)) * sizeof(KmerEntry);
fread_fix(fp, x, mem + k); k += x;
#endif
err_fclose(fp);
// bns
x = sizeof(bntseq_t); memcpy(mem + k, bns, x); k += x;
x = bns->n_holes * sizeof(bntamb1_t); memcpy(mem + k, bns->ambs, x); k += x;
x = bns->n_seqs * sizeof(bntann1_t); memcpy(mem + k, bns->anns, x); k += x;
for (i = 0; i < bns->n_seqs; ++i) {
x = strlen(bns->anns[i].name) + 1; memcpy(mem + k, bns->anns[i].name, x); k += x;
x = strlen(bns->anns[i].anno) + 1; memcpy(mem + k, bns->anns[i].anno, x); k += x;
}
// pac
x = bns->l_pac / 4 + 1;
err_fread_noeof(mem + k, 1, x, bns->fp_pac); k += x;// concatenated 2-bit encoded sequence
err_fclose(bns->fp_pac);
fprintf(stderr, "k: %ld\n", k);
return 0;
}
int main_shm(int argc, char *argv[])
{
int c, to_list = 0, to_drop = 0, ret = 0, useERT = 0;
char shm_prefix[PATH_MAX];
while ((c = getopt(argc, argv, "ldZ")) >= 0)
{
if (c == 'l') to_list = 1;
else if (c == 'd') to_drop = 1;
else if (c == 'Z') useERT = 1;
}
if (optind == argc && !to_list && !to_drop) {
fprintf(stderr, "\nUsage: fastbwa shm [-d|-l] [-f tmpFile] [idxbase]\n\n");
fprintf(stderr, "Options: -d destroy all indices in shared memory\n");
fprintf(stderr, " -l list names of indices in shared memory\n");
fprintf(stderr, " -Z use Ert as seeding index\n\n");
return 1;
}
if (optind < argc && (to_list || to_drop)) {
fprintf(stderr, "[E::%s] open -l or -d cannot be used when 'idxbase' is present\n", __func__);
return 1;
}
if (optind < argc) {
if (useERT)
sprintf(shm_prefix, "%s.ert", argv[optind]);
else
sprintf(shm_prefix, "%s", argv[optind]);
if (bwa_shm_test(shm_prefix) == 0)
{
#if 0
bwaidx_t *idx;
if (useERT)
idx = bwa_ertidx_load_from_disk(argv[optind]);
else
idx = bwa_idx_load_from_disk(argv[optind], BWA_IDX_BNS | BWA_IDX_PAC | BWA_IDX_FMT);
if (bwa_shm_stage(idx, shm_prefix, useERT) < 0) {
fprintf(stderr, "[E::%s] failed to stage the index in shared memory\n", __func__);
ret = 1;
}
bwa_idx_destroy(idx);
#else
if (useERT) {
if (bwa_shm_stage_ert(argv[optind]) < 0) {
fprintf(stderr, "[E::%s] failed to stage the index in shared memory\n", __func__);
ret = 1;
}
}
else {
if (bwa_shm_stage_fmt(argv[optind]) < 0) {
fprintf(stderr, "[E::%s] failed to stage the index in shared memory\n", __func__);
ret = 1;
}
}
#endif
}
else
fprintf(stderr, "[M::%s] index '%s' is already in shared memory\n", __func__, argv[optind]);
}
if (to_list) bwa_shm_list();
if (to_drop) bwa_shm_destroy();
return ret;
}
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