#include <string.h>
#include <unistd.h>
#include <assert.h>
+#include <pthread.h>
#include <sys/types.h>
#include "bgzf.h"
return bytes_read;
}
+/***** BEGIN: multi-threading *****/
+
+typedef struct {
+ BGZF *fp;
+ struct mtaux_t *mt;
+ void *buf;
+ int i, errcode;
+} worker_t;
+
+typedef struct mtaux_t {
+ int n_threads, n_blks, curr;
+ void **blk;
+ int *len;
+ pthread_t *tid;
+ pthread_attr_t attr;
+ worker_t *w;
+} mtaux_t;
+
+void bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks)
+{
+ int i;
+ mtaux_t *mt;
+ if (!fp->is_write || fp->mt || n_threads <= 1) return;
+ mt = calloc(1, sizeof(mtaux_t));
+ mt->n_threads = n_threads;
+ mt->n_blks = n_threads * n_sub_blks;
+ mt->blk = calloc(mt->n_blks, sizeof(void*));
+ for (i = 0; i < mt->n_blks; ++i)
+ mt->blk[i] = malloc(BGZF_MAX_BLOCK_SIZE);
+ mt->tid = calloc(mt->n_threads, sizeof(pthread_t));
+ mt->w = calloc(mt->n_threads, sizeof(worker_t));
+ for (i = 0; i < mt->n_threads; ++i) {
+ mt->w[i].i = i;
+ mt->w[i].mt = mt;
+ mt->w[i].fp = fp;
+ mt->w[i].buf = malloc(BGZF_MAX_BLOCK_SIZE);
+ }
+ pthread_attr_init(&mt->attr);
+ pthread_attr_setdetachstate(&mt->attr, PTHREAD_CREATE_JOINABLE);
+ fp->mt = mt;
+}
+
+static void mt_destroy(mtaux_t *mt)
+{
+ int i;
+ for (i = 0; i < mt->n_blks; ++i) free(mt->blk[i]);
+ for (i = 0; i < mt->n_threads; ++i) free(mt->w[i].buf);
+ free(mt->blk); free(mt->len); free(mt->w); free(mt->tid);
+ free(mt);
+}
+
+static void *mt_worker(void *data)
+{
+ int i;
+ worker_t *w = (worker_t*)data;
+ w->errcode = 0;
+ for (i = w->i; i < w->mt->curr; i += w->mt->n_threads) {
+ int clen = BGZF_MAX_BLOCK_SIZE;
+ if (bgzf_compress(w->buf, &clen, w->mt->blk[i], w->mt->len[i], w->fp->compress_level) != 0)
+ w->errcode |= BGZF_ERR_ZLIB;
+ memcpy(w->mt->blk[i], w->buf, clen);
+ w->mt->len[i] = clen;
+ }
+ return 0;
+}
+
+static int mt_flush(BGZF *fp)
+{
+ int i;
+ mtaux_t *mt = (mtaux_t*)fp->mt;
+ if (mt->curr == 0) return 0;
+ for (i = 0; i < mt->n_threads; ++i) pthread_create(&mt->tid[i], &mt->attr, mt_worker, &mt->w[i]);
+ for (i = 0; i < mt->n_threads; ++i) {
+ pthread_join(mt->tid[i], 0);
+ fp->errcode |= mt->w[i].errcode;
+ }
+ for (i = 0; i < mt->curr; ++i)
+ if (fwrite(mt->blk[i], 1, mt->len[i], fp->fp) != mt->len[i])
+ fp->errcode |= BGZF_ERR_IO;
+ mt->curr = 0;
+ return 0;
+}
+
+static int mt_push_blk(BGZF *fp)
+{
+ mtaux_t *mt = (mtaux_t*)fp->mt;
+ memcpy(mt->blk[mt->curr], fp->uncompressed_block, fp->block_offset);
+ mt->len[mt->curr] = fp->block_offset;
+ fp->block_offset = 0;
+ if (++mt->curr == mt->n_blks) mt_flush(fp);
+ return 0;
+}
+
+static ssize_t mt_write(BGZF *fp, const void *data, ssize_t length)
+{
+ const uint8_t *input = data;
+ ssize_t rest = length;
+ while (rest) {
+ int copy_length = BGZF_BLOCK_SIZE - fp->block_offset < rest? BGZF_BLOCK_SIZE - fp->block_offset : rest;
+ memcpy(fp->uncompressed_block + fp->block_offset, input, copy_length);
+ fp->block_offset += copy_length; input += copy_length; rest -= copy_length;
+ if (fp->block_offset == BGZF_BLOCK_SIZE) mt_push_blk(fp);
+ }
+ return length - rest;
+}
+
+/***** END: multi-threading *****/
+
int bgzf_flush(BGZF *fp)
{
if (!fp->is_write) return 0;
+ if (fp->mt) return mt_flush(fp);
while (fp->block_offset > 0) {
int block_length;
block_length = deflate_block(fp, fp->block_offset);
int bgzf_flush_try(BGZF *fp, ssize_t size)
{
- if (fp->block_offset + size > BGZF_BLOCK_SIZE)
- return bgzf_flush(fp);
+ if (fp->block_offset + size > BGZF_BLOCK_SIZE) {
+ if (fp->mt) return mt_push_blk(fp);
+ else return bgzf_flush(fp);
+ }
return -1;
}
ssize_t bgzf_write(BGZF *fp, const void *data, ssize_t length)
{
const uint8_t *input = data;
- int block_length = BGZF_BLOCK_SIZE, bytes_written;
+ int block_length = BGZF_BLOCK_SIZE, bytes_written = 0;
assert(fp->is_write);
- input = data;
- bytes_written = 0;
+ if (fp->mt) return mt_write(fp, data, length);
while (bytes_written < length) {
uint8_t* buffer = fp->uncompressed_block;
int copy_length = block_length - fp->block_offset < length - bytes_written? block_length - fp->block_offset : length - bytes_written;
if (fp == 0) return -1;
if (fp->is_write) {
if (bgzf_flush(fp) != 0) return -1;
+ fp->compress_level = -1;
block_length = deflate_block(fp, 0); // write an empty block
count = fwrite(fp->compressed_block, 1, block_length, fp->fp);
if (fflush(fp->fp) != 0) {
fp->errcode |= BGZF_ERR_IO;
return -1;
}
+ if (fp->mt) mt_destroy(fp->mt);
}
ret = fp->is_write? fclose(fp->fp) : _bgzf_close(fp->fp);
if (ret != 0) return -1;