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 ai<bi? -1 : ai>bi? 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
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);
}
@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;
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) {
}
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) {
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;
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) {
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 <out.bam> [in1.bam]\n\n");
fprintf(stderr, "Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users\n");
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 <pthread.h>
+
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
@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);
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 <maxMem>] <in.bam> <out.prefix>\n");
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: samtools sort [options] <in.bam> <out.prefix>\n\n");
+ fprintf(stderr, "Options: -n sort by read name\n");
+ fprintf(stderr, " -f use <out.prefix> 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;
}
projects / rsem.git / blobdiff