From 9d415a46d92d1d43286cc59c5bb0b47085a9d33e Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sun, 18 Mar 2012 17:15:30 -0400 Subject: [PATCH] multi-threaded sorting --- bam_sort.c | 196 ++++++++++++++++++++++++++++++++--------------------- 1 file changed, 117 insertions(+), 79 deletions(-) diff --git a/bam_sort.c b/bam_sort.c index f436fb9..166be2a 100644 --- a/bam_sort.c +++ b/bam_sort.c @@ -308,6 +308,12 @@ int bam_merge(int argc, char *argv[]) return ret; } +/*************** + * BAM sorting * + ***************/ + +#include + typedef bam1_t *bam1_p; static inline int bam1_lt(const bam1_p a, const bam1_p b) @@ -319,34 +325,69 @@ static inline int bam1_lt(const bam1_p a, const bam1_p b) } KSORT_INIT(sort, bam1_p, bam1_lt) -static void sort_blocks(int n, int k, bam1_p *buf, const char *prefix, const bam_header_t *h, int is_stdout) +typedef struct { + size_t buf_len; + const char *prefix; + bam1_p *buf; + const bam_header_t *h; + int index; +} worker_t; + +static void write_buffer(const char *fn, const char *mode, size_t l, bam1_p *buf, const bam_header_t *h, int n_threads) { - char *name, mode[3]; - int i; + size_t i; bamFile fp; - ks_mergesort(sort, k, buf, 0); - name = (char*)calloc(strlen(prefix) + 20, 1); - if (n >= 0) { - sprintf(name, "%s.%.4d.bam", prefix, n); - strcpy(mode, "w1"); - } else { - sprintf(name, "%s.bam", prefix); - strcpy(mode, "w"); - } - fp = is_stdout? bam_dopen(fileno(stdout), mode) : bam_open(name, mode); - if (fp == 0) { - fprintf(stderr, "[sort_blocks] fail to create file %s.\n", name); - free(name); - // FIXME: possible memory leak - return; - } - free(name); + fp = strcmp(fn, "-")? bam_open(fn, mode) : bam_dopen(fileno(stdout), mode); + if (fp == 0) return; bam_header_write(fp, h); - for (i = 0; i < k; ++i) + if (n_threads > 1) bgzf_mt(fp, n_threads, 256); + for (i = 0; i < l; ++i) bam_write1_core(fp, &buf[i]->core, buf[i]->data_len, buf[i]->data); bam_close(fp); } +static void *worker(void *data) +{ + worker_t *w = (worker_t*)data; + char *name; + ks_mergesort(sort, w->buf_len, w->buf, 0); + name = (char*)calloc(strlen(w->prefix) + 20, 1); + sprintf(name, "%s.%.4d.bam", w->prefix, w->index); + write_buffer(name, "w1", w->buf_len, w->buf, w->h, 0); + free(name); + return 0; +} + +static int sort_blocks(int n_files, size_t k, bam1_p *buf, const char *prefix, const bam_header_t *h, int n_threads) +{ + int i; + size_t rest; + bam1_p *b; + pthread_t *tid; + pthread_attr_t attr; + worker_t *w; + + if (n_threads < 1) n_threads = 1; + if (k < n_threads * 64) n_threads = 1; // use a single thread if we only sort a small batch of records + pthread_attr_init(&attr); + pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE); + w = calloc(n_threads, sizeof(worker_t)); + tid = calloc(n_threads, sizeof(pthread_t)); + b = buf; rest = k; + for (i = 0; i < n_threads; ++i) { + w[i].buf_len = rest / (n_threads - i); + w[i].buf = b; + w[i].prefix = prefix; + w[i].h = h; + w[i].index = n_files + i; + b += w[i].buf_len; rest -= w[i].buf_len; + pthread_create(&tid[i], &attr, worker, &w[i]); + } + for (i = 0; i < n_threads; ++i) pthread_join(tid[i], 0); + free(tid); free(w); + return n_files + n_threads; +} + /*! @abstract Sort an unsorted BAM file based on the chromosome order and the leftmost position of an alignment @@ -361,63 +402,77 @@ static void sort_blocks(int n, int k, bam1_p *buf, const char *prefix, const bam and then merge them by calling bam_merge_core(). This function is NOT thread safe. */ -void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t max_mem, int is_stdout) +void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t _max_mem, int is_stdout, int n_threads) { - int n, ret, k, i; - size_t mem; + int ret, i, extra_mem, n_files = 0; + size_t mem, max_k, k, max_mem; bam_header_t *header; bamFile fp; bam1_t *b, **buf; + char *fnout = 0; + if (n_threads < 2) n_threads = 1; + extra_mem = sizeof(void*) + sizeof(void*) + (sizeof(bam1_t) - sizeof(bam1_core_t)); g_is_by_qname = is_by_qname; - n = k = 0; mem = 0; + max_k = k = 0; mem = 0; + max_mem = _max_mem * n_threads; + buf = 0; fp = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r"); if (fp == 0) { fprintf(stderr, "[bam_sort_core] fail to open file %s\n", fn); return; } header = bam_header_read(fp); - buf = (bam1_t**)calloc(max_mem / BAM_CORE_SIZE, sizeof(bam1_t*)); // write sub files for (;;) { + if (k == max_k) { + size_t old_max = max_k; + max_k = max_k? max_k<<1 : 0x10000; + buf = realloc(buf, max_k * sizeof(void*)); + memset(buf + old_max, 0, sizeof(void*) * (max_k - old_max)); + } if (buf[k] == 0) buf[k] = (bam1_t*)calloc(1, sizeof(bam1_t)); b = buf[k]; if ((ret = bam_read1(fp, b)) < 0) break; - mem += ret; + mem += ret + extra_mem; ++k; if (mem >= max_mem) { - sort_blocks(n++, k, buf, prefix, header, 0); - mem = 0; k = 0; + n_files = sort_blocks(n_files, k, buf, prefix, header, n_threads); + mem = k = 0; } } if (ret != -1) fprintf(stderr, "[bam_sort_core] truncated file. Continue anyway.\n"); - if (n == 0) sort_blocks(-1, k, buf, prefix, header, is_stdout); - else { // then merge - char **fns, *fnout; - fprintf(stderr, "[bam_sort_core] merging from %d files...\n", n+1); - sort_blocks(n++, k, buf, prefix, header, 0); - fnout = (char*)calloc(strlen(prefix) + 20, 1); - if (is_stdout) sprintf(fnout, "-"); - else sprintf(fnout, "%s.bam", prefix); - fns = (char**)calloc(n, sizeof(char*)); - for (i = 0; i < n; ++i) { + // output file name + fnout = calloc(strlen(prefix) + 20, 1); + if (is_stdout) sprintf(fnout, "-"); + else sprintf(fnout, "%s.bam", prefix); + // write the final output + if (n_files == 0) { // a single block + ks_mergesort(sort, k, buf, 0); + write_buffer(fnout, "w", k, buf, header, n_threads); + } else { // then merge + char **fns; + n_files = sort_blocks(n_files, k, buf, prefix, header, n_threads); + fprintf(stderr, "[bam_sort_core] merging from %d files...\n", n_files); + fns = (char**)calloc(n_files, sizeof(char*)); + for (i = 0; i < n_files; ++i) { fns[i] = (char*)calloc(strlen(prefix) + 20, 1); sprintf(fns[i], "%s.%.4d.bam", prefix, i); } - bam_merge_core(is_by_qname, fnout, 0, n, fns, 0, 0); - free(fnout); - for (i = 0; i < n; ++i) { + bam_merge_core2(is_by_qname, fnout, 0, n_files, fns, 0, 0, n_threads); + for (i = 0; i < n_files; ++i) { unlink(fns[i]); free(fns[i]); } free(fns); } - for (k = 0; k < max_mem / BAM_CORE_SIZE; ++k) { - if (buf[k]) { - free(buf[k]->data); - free(buf[k]); - } + free(fnout); + // free + for (k = 0; k < max_k; ++k) { + if (!buf[k]) continue; + free(buf[k]->data); + free(buf[k]); } free(buf); bam_header_destroy(header); @@ -426,49 +481,32 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem) { - bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0); -} - - -size_t bam_sort_get_max_mem(char *max_mem_string) -{ - char c; - size_t max_mem; - size_t multiplier=1; - c=max_mem_string[strlen(max_mem_string)-1]; - switch(c) { - case 'G': - multiplier*=1024; - case 'M': - multiplier*=1024; - case 'K': - multiplier*=1024; - case 'B': - max_mem_string[strlen(max_mem_string)-1]='\0'; - break; - default: - break; - } - max_mem = multiplier * atol(max_mem_string); - // max_mem should be checked that it was not zero after atol! - return max_mem; + bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0, 0); } int bam_sort(int argc, char *argv[]) { - size_t max_mem = 500000000; - int c, is_by_qname = 0, is_stdout = 0; - while ((c = getopt(argc, argv, "nom:")) >= 0) { + size_t max_mem = 1<<29; // 512MB + int c, is_by_qname = 0, is_stdout = 0, n_threads = 0; + while ((c = getopt(argc, argv, "nom:@:")) >= 0) { switch (c) { case 'o': is_stdout = 1; break; case 'n': is_by_qname = 1; break; - case 'm': max_mem = bam_sort_get_max_mem(optarg); break; + case 'm': { + char *q; + max_mem = strtol(optarg, &q, 0); + if (*q == 'k' || *q == 'K') max_mem <<= 10; + else if (*q == 'm' || *q == 'M') max_mem <<= 20; + else if (*q == 'g' || *q == 'G') max_mem <<= 30; + break; + } + case '@': n_threads = atoi(optarg); break; } } if (optind + 2 > argc) { - fprintf(stderr, "Usage: samtools sort [-on] [-m ] \n"); + fprintf(stderr, "Usage: samtools sort [-on] [-m maxMem=1G] \n"); return 1; } - bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout); + bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads); return 0; } -- 2.39.2