#include <stdlib.h>
#include <ctype.h>
#include <assert.h>
+#include <errno.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
typedef struct {
int i;
- uint64_t pos;
+ uint64_t pos, idx;
bam1_t *b;
} heap1_t;
+#define __pos_cmp(a, b) ((a).pos > (b).pos || ((a).pos == (b).pos && ((a).i > (b).i || ((a).i == (b).i && (a).idx > (b).idx))))
+
static inline int heap_lt(const heap1_t a, const heap1_t b)
{
if (g_is_by_qname) {
- int t = strnum_cmp(bam1_qname(a.b), bam1_qname(b.b));
- return (t > 0 || (t == 0 && a.pos > b.pos));
- } else return (a.pos > b.pos);
+ 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)));
+ } else return __pos_cmp(a, b);
}
KSORT_INIT(heap, heap1_t, heap_lt)
+static void swap_header_targets(bam_header_t *h1, bam_header_t *h2)
+{
+ bam_header_t t;
+ t.n_targets = h1->n_targets, h1->n_targets = h2->n_targets, h2->n_targets = t.n_targets;
+ t.target_name = h1->target_name, h1->target_name = h2->target_name, h2->target_name = t.target_name;
+ t.target_len = h1->target_len, h1->target_len = h2->target_len, h2->target_len = t.target_len;
+}
+
+static void swap_header_text(bam_header_t *h1, bam_header_t *h2)
+{
+ int tempi;
+ char *temps;
+ tempi = h1->l_text, h1->l_text = h2->l_text, h2->l_text = tempi;
+ temps = h1->text, h1->text = h2->text, h2->text = temps;
+}
+
+#define MERGE_RG 1
+#define MERGE_UNCOMP 2
+#define MERGE_LEVEL1 4
+#define MERGE_FORCE 8
+
/*!
@abstract Merge multiple sorted BAM.
@param is_by_qname whether to sort by query name
@param out output BAM file name
+ @param headers name of SAM file from which to copy '@' header lines,
+ or NULL to copy them from the first file to be merged
@param n number of files to be merged
@param fn names of files to be merged
@discussion Padding information may NOT correctly maintained. This
function is NOT thread safe.
*/
-void bam_merge_core(int by_qname, const char *out, int n, char * const *fn)
+int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn,
+ int flag, const char *reg)
{
bamFile fpout, *fp;
heap1_t *heap;
bam_header_t *hout = 0;
- int i, j;
+ bam_header_t *hheaders = NULL;
+ int i, j, *RG_len = 0;
+ uint64_t idx = 0;
+ char **RG = 0;
+ bam_iter_t *iter = 0;
+
+ if (headers) {
+ tamFile fpheaders = sam_open(headers);
+ if (fpheaders == 0) {
+ const char *message = strerror(errno);
+ fprintf(stderr, "[bam_merge_core] cannot open '%s': %s\n", headers, message);
+ return -1;
+ }
+ hheaders = sam_header_read(fpheaders);
+ sam_close(fpheaders);
+ }
g_is_by_qname = by_qname;
fp = (bamFile*)calloc(n, sizeof(bamFile));
heap = (heap1_t*)calloc(n, sizeof(heap1_t));
+ iter = (bam_iter_t*)calloc(n, sizeof(bam_iter_t));
+ // prepare RG tag
+ if (flag & MERGE_RG) {
+ RG = (char**)calloc(n, sizeof(void*));
+ RG_len = (int*)calloc(n, sizeof(int));
+ for (i = 0; i != n; ++i) {
+ int l = strlen(fn[i]);
+ const char *s = fn[i];
+ if (l > 4 && strcmp(s + l - 4, ".bam") == 0) l -= 4;
+ for (j = l - 1; j >= 0; --j) if (s[j] == '/') break;
+ ++j; l -= j;
+ RG[i] = calloc(l + 1, 1);
+ RG_len[i] = l;
+ strncpy(RG[i], s + j, l);
+ }
+ }
+ // read the first
for (i = 0; i != n; ++i) {
- heap1_t *h;
bam_header_t *hin;
- assert(fp[i] = bam_open(fn[i], "r"));
+ fp[i] = bam_open(fn[i], "r");
+ if (fp[i] == 0) {
+ int j;
+ fprintf(stderr, "[bam_merge_core] fail to open file %s\n", fn[i]);
+ for (j = 0; j < i; ++j) bam_close(fp[j]);
+ free(fp); free(heap);
+ // FIXME: possible memory leak
+ return -1;
+ }
hin = bam_header_read(fp[i]);
- if (i == 0) hout = hin;
- else { // validate multiple baf
- if (hout->n_targets != hin->n_targets) {
- fprintf(stderr, "[bam_merge_core] file '%s' has different number of target sequences. Abort!\n", fn[i]);
- exit(1);
- }
- for (j = 0; j < hout->n_targets; ++j) {
- if (strcmp(hout->target_name[j], hin->target_name[j])) {
- fprintf(stderr, "[bam_merge_core] different target sequence name: '%s' != '%s' in file '%s'. Abort!\n",
+ if (i == 0) { // the first BAM
+ hout = hin;
+ } else { // validate multiple baf
+ int min_n_targets = hout->n_targets;
+ if (hin->n_targets < min_n_targets) min_n_targets = hin->n_targets;
+
+ for (j = 0; j < min_n_targets; ++j)
+ if (strcmp(hout->target_name[j], hin->target_name[j]) != 0) {
+ fprintf(stderr, "[bam_merge_core] different target sequence name: '%s' != '%s' in file '%s'\n",
hout->target_name[j], hin->target_name[j], fn[i]);
- exit(1);
+ return -1;
}
- if (hout->target_len[j] != hin->target_len[j])
- fprintf(stderr, "[bam_merge_core] different target sequence length: %d != %d in file '%s'. Continue.\n",
- hout->target_len[j], hin->target_len[j], fn[i]);
+
+ // If this input file has additional target reference sequences,
+ // add them to the headers to be output
+ if (hin->n_targets > hout->n_targets) {
+ swap_header_targets(hout, hin);
+ // FIXME Possibly we should also create @SQ text headers
+ // for the newly added reference sequences
}
+
bam_header_destroy(hin);
}
- h = heap + i;
+ }
+
+ if (hheaders) {
+ // If the text headers to be swapped in include any @SQ headers,
+ // check that they are consistent with the existing binary list
+ // of reference information.
+ if (hheaders->n_targets > 0) {
+ if (hout->n_targets != hheaders->n_targets) {
+ fprintf(stderr, "[bam_merge_core] number of @SQ headers in '%s' differs from number of target sequences\n", headers);
+ if (!reg) return -1;
+ }
+ for (j = 0; j < hout->n_targets; ++j)
+ if (strcmp(hout->target_name[j], hheaders->target_name[j]) != 0) {
+ fprintf(stderr, "[bam_merge_core] @SQ header '%s' in '%s' differs from target sequence\n", hheaders->target_name[j], headers);
+ if (!reg) return -1;
+ }
+ }
+
+ swap_header_text(hout, hheaders);
+ bam_header_destroy(hheaders);
+ }
+
+ if (reg) {
+ int tid, beg, end;
+ if (bam_parse_region(hout, reg, &tid, &beg, &end) < 0) {
+ fprintf(stderr, "[%s] Malformated region string or undefined reference name\n", __func__);
+ return -1;
+ }
+ for (i = 0; i < n; ++i) {
+ bam_index_t *idx;
+ idx = bam_index_load(fn[i]);
+ iter[i] = bam_iter_query(idx, tid, beg, end);
+ bam_index_destroy(idx);
+ }
+ }
+
+ for (i = 0; i < n; ++i) {
+ heap1_t *h = heap + i;
h->i = i;
h->b = (bam1_t*)calloc(1, sizeof(bam1_t));
- if (bam_read1(fp[i], h->b) >= 0)
- h->pos = ((uint64_t)h->b->core.tid<<32) | (uint32_t)h->b->core.pos<<1 | bam1_strand(h->b);
+ if (bam_iter_read(fp[i], iter[i], h->b) >= 0) {
+ h->pos = ((uint64_t)h->b->core.tid<<32) | (uint32_t)((int32_t)h->b->core.pos+1)<<1 | bam1_strand(h->b);
+ h->idx = idx++;
+ }
else h->pos = HEAP_EMPTY;
}
- fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w");
- assert(fpout);
+ 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) {
+ fprintf(stderr, "[%s] fail to create the output file.\n", __func__);
+ return -1;
+ }
bam_header_write(fpout, hout);
bam_header_destroy(hout);
ks_heapmake(heap, n, heap);
while (heap->pos != HEAP_EMPTY) {
bam1_t *b = heap->b;
+ if (flag & MERGE_RG) {
+ uint8_t *rg = bam_aux_get(b, "RG");
+ if (rg) bam_aux_del(b, rg);
+ bam_aux_append(b, "RG", 'Z', RG_len[heap->i] + 1, (uint8_t*)RG[heap->i]);
+ }
bam_write1_core(fpout, &b->core, b->data_len, b->data);
- if ((j = bam_read1(fp[heap->i], b)) >= 0)
- heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)b->core.pos<<1 | bam1_strand(b);
- else if (j == -1) heap->pos = HEAP_EMPTY;
- else fprintf(stderr, "[bam_merge_core] '%s' is truncated. Continue anyway.\n", fn[heap->i]);
+ if ((j = bam_iter_read(fp[heap->i], iter[heap->i], b)) >= 0) {
+ heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)((int)b->core.pos+1)<<1 | bam1_strand(b);
+ heap->idx = idx++;
+ } else if (j == -1) {
+ heap->pos = HEAP_EMPTY;
+ free(heap->b->data); free(heap->b);
+ heap->b = 0;
+ } else fprintf(stderr, "[bam_merge_core] '%s' is truncated. Continue anyway.\n", fn[heap->i]);
ks_heapadjust(heap, 0, n, heap);
}
+ if (flag & MERGE_RG) {
+ for (i = 0; i != n; ++i) free(RG[i]);
+ free(RG); free(RG_len);
+ }
for (i = 0; i != n; ++i) {
+ bam_iter_destroy(iter[i]);
bam_close(fp[i]);
- free(heap[i].b->data);
- free(heap[i].b);
}
bam_close(fpout);
- free(fp); free(heap);
+ free(fp); free(heap); free(iter);
+ return 0;
}
+
int bam_merge(int argc, char *argv[])
{
- int c, is_by_qname = 0;
- while ((c = getopt(argc, argv, "n")) >= 0) {
+ int c, is_by_qname = 0, flag = 0, ret = 0;
+ char *fn_headers = NULL, *reg = 0;
+
+ while ((c = getopt(argc, argv, "h:nru1R:f")) >= 0) {
switch (c) {
+ case 'r': flag |= MERGE_RG; break;
+ case 'f': flag |= MERGE_FORCE; break;
+ case 'h': fn_headers = strdup(optarg); break;
case 'n': is_by_qname = 1; break;
+ case '1': flag |= MERGE_LEVEL1; break;
+ case 'u': flag |= MERGE_UNCOMP; break;
+ case 'R': reg = strdup(optarg); break;
}
}
if (optind + 2 >= argc) {
- fprintf(stderr, "Usage: samtools merge [-n] <out.bam> <in1.bam> <in2.bam> [...]\n");
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: samtools merge [-nr] [-h inh.sam] <out.bam> <in1.bam> <in2.bam> [...]\n\n");
+ fprintf(stderr, "Options: -n sort by read names\n");
+ fprintf(stderr, " -r attach RG tag (inferred from file names)\n");
+ 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, " -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");
+ fprintf(stderr, " must provide the correct header with -h, or uses Picard which properly maintains\n");
+ fprintf(stderr, " the header dictionary in merging.\n\n");
return 1;
}
- bam_merge_core(is_by_qname, argv[optind], argc - optind - 1, argv + optind + 1);
- return 0;
+ if (!(flag & MERGE_FORCE) && strcmp(argv[optind], "-")) {
+ FILE *fp = fopen(argv[optind], "rb");
+ if (fp != NULL) {
+ fclose(fp);
+ fprintf(stderr, "[%s] File '%s' exists. Please apply '-f' to overwrite. Abort.\n", __func__, argv[optind]);
+ return 1;
+ }
+ }
+ if (bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg) < 0) ret = 1;
+ free(reg);
+ free(fn_headers);
+ return ret;
}
typedef bam1_t *bam1_p;
{
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) < ((uint64_t)b->core.tid<<32|b->core.pos))));
- } else return (((uint64_t)a->core.tid<<32|a->core.pos) < ((uint64_t)b->core.tid<<32|b->core.pos));
+ 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)));
}
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)
+static void sort_blocks(int n, int k, bam1_p *buf, const char *prefix, const bam_header_t *h, int is_stdout)
{
- char *name;
+ char *name, mode[3];
int 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);
- else sprintf(name, "%s.bam", prefix);
- assert(fp = bam_open(name, "w"));
+ 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);
bam_header_write(fp, h);
for (i = 0; i < k; ++i)
and then merge them by calling bam_merge_core(). This function is
NOT thread safe.
*/
-void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem)
+void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t max_mem, int is_stdout)
{
int n, ret, k, i;
size_t mem;
g_is_by_qname = is_by_qname;
n = k = 0; mem = 0;
fp = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
- assert(fp);
+ 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
mem += ret;
++k;
if (mem >= max_mem) {
- sort_blocks(n++, k, buf, prefix, header);
+ sort_blocks(n++, k, buf, prefix, header, 0);
mem = 0; 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);
+ 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);
+ sort_blocks(n++, k, buf, prefix, header, 0);
fnout = (char*)calloc(strlen(prefix) + 20, 1);
- sprintf(fnout, "%s.bam", prefix);
+ if (is_stdout) sprintf(fnout, "-");
+ else sprintf(fnout, "%s.bam", prefix);
fns = (char**)calloc(n, sizeof(char*));
for (i = 0; i < n; ++i) {
fns[i] = (char*)calloc(strlen(prefix) + 20, 1);
sprintf(fns[i], "%s.%.4d.bam", prefix, i);
}
- bam_merge_core(is_by_qname, fnout, n, fns);
+ bam_merge_core(is_by_qname, fnout, 0, n, fns, 0, 0);
free(fnout);
for (i = 0; i < n; ++i) {
unlink(fns[i]);
bam_close(fp);
}
+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);
+}
+
int bam_sort(int argc, char *argv[])
{
size_t max_mem = 500000000;
- int c, is_by_qname = 0;
- while ((c = getopt(argc, argv, "nm:")) >= 0) {
+ int c, is_by_qname = 0, is_stdout = 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 = atol(optarg); break;
}
}
if (optind + 2 > argc) {
- fprintf(stderr, "Usage: samtools sort [-n] [-m <maxMem>] <in.bam> <out.prefix>\n");
+ fprintf(stderr, "Usage: samtools sort [-on] [-m <maxMem>] <in.bam> <out.prefix>\n");
return 1;
}
- bam_sort_core(is_by_qname, argv[optind], argv[optind+1], max_mem);
+ bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout);
return 0;
}
projects / samtools.git / blobdiff