X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=sam%2Fbam_sort.c;h=c46bce3b3f4ab2fbc5e5166b4bfaf2ff12b013a9;hp=abf8d4f6caf6dfeb25af423784934d78fe677478;hb=dbcf1cfb8ad1086c21d64e249f012809403e7ddc;hpb=58d504aaf36ae486b1dba6d03e0e9f1c25855037 diff --git a/sam/bam_sort.c b/sam/bam_sort.c index abf8d4f..c46bce3 100644 --- a/sam/bam_sort.c +++ b/sam/bam_sort.c @@ -10,24 +10,28 @@ static int g_is_by_qname = 0; -static inline int strnum_cmp(const char *a, const char *b) +static int strnum_cmp(const char *_a, const char *_b) { - char *pa, *pb; - pa = (char*)a; pb = (char*)b; + const unsigned char *a = (const unsigned char*)_a, *b = (const unsigned char*)_b; + const unsigned char *pa = a, *pb = b; while (*pa && *pb) { if (isdigit(*pa) && isdigit(*pb)) { - long ai, bi; - ai = strtol(pa, &pa, 10); - bi = strtol(pb, &pb, 10); - if (ai != bi) return aibi? 1 : 0; + while (*pa == '0') ++pa; + while (*pb == '0') ++pb; + while (isdigit(*pa) && isdigit(*pb) && *pa == *pb) ++pa, ++pb; + if (isdigit(*pa) && isdigit(*pb)) { + int i = 0; + while (isdigit(pa[i]) && isdigit(pb[i])) ++i; + return isdigit(pa[i])? 1 : isdigit(pb[i])? -1 : (int)*pa - (int)*pb; + } else if (isdigit(*pa)) return 1; + else if (isdigit(*pb)) return -1; + else if (pa - a != pb - b) return pa - a < pb - b? 1 : -1; } else { - if (*pa != *pb) break; + if (*pa != *pb) return (int)*pa - (int)*pb; ++pa; ++pb; } } - if (*pa == *pb) - return (pa-a) < (pb-b)? -1 : (pa-a) > (pb-b)? 1 : 0; - return *pa<*pb? -1 : *pa>*pb? 1 : 0; + return *pa? 1 : *pb? -1 : 0; } #define HEAP_EMPTY 0xffffffffffffffffull @@ -46,7 +50,7 @@ static inline int heap_lt(const heap1_t a, const heap1_t b) int t; if (a.b == 0 || b.b == 0) return a.b == 0? 1 : 0; t = strnum_cmp(bam1_qname(a.b), bam1_qname(b.b)); - return (t > 0 || (t == 0 && __pos_cmp(a, b))); + return (t > 0 || (t == 0 && (a.b->core.flag&0xc0) > (b.b->core.flag&0xc0))); } else return __pos_cmp(a, b); } @@ -85,8 +89,7 @@ static void swap_header_text(bam_header_t *h1, bam_header_t *h2) @discussion Padding information may NOT correctly maintained. This function is NOT thread safe. */ -int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, - int flag, const char *reg) +int bam_merge_core2(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg, int n_threads, int level) { bamFile fpout, *fp; heap1_t *heap; @@ -94,7 +97,7 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch bam_header_t *hheaders = NULL; int i, j, *RG_len = 0; uint64_t idx = 0; - char **RG = 0; + char **RG = 0, mode[8]; bam_iter_t *iter = 0; if (headers) { @@ -209,15 +212,17 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch } else h->pos = HEAP_EMPTY; } - if (flag & MERGE_UNCOMP) fpout = strcmp(out, "-")? bam_open(out, "wu") : bam_dopen(fileno(stdout), "wu"); - else if (flag & MERGE_LEVEL1) fpout = strcmp(out, "-")? bam_open(out, "w1") : bam_dopen(fileno(stdout), "w1"); - else fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w"); - if (fpout == 0) { + if (flag & MERGE_UNCOMP) level = 0; + else if (flag & MERGE_LEVEL1) level = 1; + strcpy(mode, "w"); + if (level >= 0) sprintf(mode + 1, "%d", level < 9? level : 9); + if ((fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w")) == 0) { fprintf(stderr, "[%s] fail to create the output file.\n", __func__); return -1; } bam_header_write(fpout, hout); bam_header_destroy(hout); + if (!(flag & MERGE_UNCOMP)) bgzf_mt(fpout, n_threads, 256); ks_heapmake(heap, n, heap); while (heap->pos != HEAP_EMPTY) { @@ -252,12 +257,17 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch return 0; } +int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg) +{ + return bam_merge_core2(by_qname, out, headers, n, fn, flag, reg, 0, -1); +} + int bam_merge(int argc, char *argv[]) { - int c, is_by_qname = 0, flag = 0, ret = 0; + int c, is_by_qname = 0, flag = 0, ret = 0, n_threads = 0, level = -1; char *fn_headers = NULL, *reg = 0; - while ((c = getopt(argc, argv, "h:nru1R:f")) >= 0) { + while ((c = getopt(argc, argv, "h:nru1R:f@:l:")) >= 0) { switch (c) { case 'r': flag |= MERGE_RG; break; case 'f': flag |= MERGE_FORCE; break; @@ -266,6 +276,8 @@ int bam_merge(int argc, char *argv[]) case '1': flag |= MERGE_LEVEL1; break; case 'u': flag |= MERGE_UNCOMP; break; case 'R': reg = strdup(optarg); break; + case 'l': level = atoi(optarg); break; + case '@': n_threads = atoi(optarg); break; } } if (optind + 2 >= argc) { @@ -276,6 +288,8 @@ int bam_merge(int argc, char *argv[]) fprintf(stderr, " -u uncompressed BAM output\n"); fprintf(stderr, " -f overwrite the output BAM if exist\n"); fprintf(stderr, " -1 compress level 1\n"); + fprintf(stderr, " -l INT compression level, from 0 to 9 [-1]\n"); + fprintf(stderr, " -@ INT number of BAM compression threads [0]\n"); fprintf(stderr, " -R STR merge file in the specified region STR [all]\n"); fprintf(stderr, " -h FILE copy the header in FILE to [in1.bam]\n\n"); fprintf(stderr, "Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users\n"); @@ -291,51 +305,126 @@ int bam_merge(int argc, char *argv[]) return 1; } } - if (bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg) < 0) ret = 1; + if (bam_merge_core2(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg, n_threads, level) < 0) ret = 1; free(reg); free(fn_headers); return ret; } +/*************** + * BAM sorting * + ***************/ + +#include + typedef bam1_t *bam1_p; +static int change_SO(bam_header_t *h, const char *so) +{ + char *p, *q, *beg = 0, *end = 0, *newtext; + if (h->l_text > 3) { + if (strncmp(h->text, "@HD", 3) == 0) { + if ((p = strchr(h->text, '\n')) == 0) return -1; + *p = '\0'; + if ((q = strstr(h->text, "\tSO:")) != 0) { + *p = '\n'; // change back + if (strncmp(q + 4, so, p - q - 4) != 0) { + beg = q; + for (q += 4; *q != '\n' && *q != '\t'; ++q); + end = q; + } else return 0; // no need to change + } else beg = end = p, *p = '\n'; + } + } + if (beg == 0) { // no @HD + h->l_text += strlen(so) + 15; + newtext = malloc(h->l_text + 1); + sprintf(newtext, "@HD\tVN:1.3\tSO:%s\n", so); + strcat(newtext, h->text); + } else { // has @HD but different or no SO + h->l_text = (beg - h->text) + (4 + strlen(so)) + (h->text + h->l_text - end); + newtext = malloc(h->l_text + 1); + strncpy(newtext, h->text, beg - h->text); + sprintf(newtext + (beg - h->text), "\tSO:%s", so); + strcat(newtext, end); + } + free(h->text); + h->text = newtext; + return 0; +} + static inline int bam1_lt(const bam1_p a, const bam1_p b) { if (g_is_by_qname) { int t = strnum_cmp(bam1_qname(a), bam1_qname(b)); - return (t < 0 || (t == 0 && (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1))))); - } else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1))); + return (t < 0 || (t == 0 && (a->core.flag&0xc0) < (b->core.flag&0xc0))); + } else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)<<1|bam1_strand(a)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)<<1|bam1_strand(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 @@ -345,68 +434,94 @@ static void sort_blocks(int n, int k, bam1_p *buf, const char *prefix, const bam @param prefix prefix of the output and the temporary files; upon sucessess, prefix.bam will be written. @param max_mem approxiate maximum memory (very inaccurate) + @param full_path the given output path is the full path and not just the prefix @discussion It may create multiple temporary subalignment files 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 level, int full_path) { - int n, ret, k, i; - size_t mem; + int ret, i, n_files = 0; + size_t mem, max_k, k, max_mem; bam_header_t *header; bamFile fp; bam1_t *b, **buf; + char *fnout = 0; + char const *suffix = ".bam"; + if (full_path) suffix += 4; + if (n_threads < 2) n_threads = 1; 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*)); + if (is_by_qname) change_SO(header, "queryname"); + else change_SO(header, "coordinate"); // 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; + if (b->data_len < b->m_data>>2) { // shrink + b->m_data = b->data_len; + kroundup32(b->m_data); + b->data = realloc(b->data, b->m_data); + } + mem += sizeof(bam1_t) + b->m_data + sizeof(void*) + sizeof(void*); // two sizeof(void*) for the data allocated to pointer arrays ++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%s", prefix, suffix); + // write the final output + if (n_files == 0) { // a single block + char mode[8]; + strcpy(mode, "w"); + if (level >= 0) sprintf(mode + 1, "%d", level < 9? level : 9); + ks_mergesort(sort, k, buf, 0); + write_buffer(fnout, mode, 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); + sprintf(fns[i], "%s.%.4d%s", prefix, i, suffix); } - 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, level); + 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); @@ -415,24 +530,42 @@ 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); + bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0, 0, -1, 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 = 768<<20; // 512MB + int c, is_by_qname = 0, is_stdout = 0, n_threads = 0, level = -1, full_path = 0; + while ((c = getopt(argc, argv, "fnom:@:l:")) >= 0) { switch (c) { + case 'f': full_path = 1; break; case 'o': is_stdout = 1; break; case 'n': is_by_qname = 1; break; - case 'm': max_mem = atol(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; + case 'l': level = atoi(optarg); break; } } if (optind + 2 > argc) { - fprintf(stderr, "Usage: samtools sort [-on] [-m ] \n"); + fprintf(stderr, "\n"); + fprintf(stderr, "Usage: samtools sort [options] \n\n"); + fprintf(stderr, "Options: -n sort by read name\n"); + fprintf(stderr, " -f use as full file name instead of prefix\n"); + fprintf(stderr, " -o final output to stdout\n"); + fprintf(stderr, " -l INT compression level, from 0 to 9 [-1]\n"); + fprintf(stderr, " -@ INT number of sorting and compression threads [1]\n"); + fprintf(stderr, " -m INT max memory per thread; suffix K/M/G recognized [768M]\n"); + fprintf(stderr, "\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, level, full_path); return 0; }