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));
+ 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 && a.pos > b.pos));
} else return (a.pos > b.pos);
}
KSORT_INIT(heap, heap1_t, heap_lt)
+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;
+}
+
/*!
@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)
+void bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn)
{
bamFile fpout, *fp;
heap1_t *heap;
bam_header_t *hout = 0;
+ bam_header_t *hheaders = NULL;
int i, j;
+ if (headers) {
+ tamFile fpheaders = sam_open(headers);
+ if (fpheaders == 0) {
+ fprintf(stderr, "[bam_merge_core] Cannot open file `%s'. Continue anyway.\n", headers);
+ } else {
+ 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));
bam_header_t *hin;
assert(fp[i] = bam_open(fn[i], "r"));
hin = bam_header_read(fp[i]);
- if (i == 0) hout = hin;
- else { // validate multiple baf
+ if (i == 0) { // the first SAM
+ hout = hin;
+ 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", headers);
+ 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", hheaders->target_name[j], headers);
+ }
+ swap_header_text(hout, hheaders);
+ bam_header_destroy(hheaders);
+ hheaders = NULL;
+ }
+ } 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);
hout->target_name[j], hin->target_name[j], fn[i]);
exit(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]);
}
bam_header_destroy(hin);
}
while (heap->pos != HEAP_EMPTY) {
bam1_t *b = heap->b;
bam_write1_core(fpout, &b->core, b->data_len, b->data);
- if ((j = bam_read1(fp[heap->i], b)) >= 0)
+ 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]);
+ } 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);
}
- for (i = 0; i != n; ++i) {
- bam_close(fp[i]);
- free(heap[i].b->data);
- free(heap[i].b);
- }
+ for (i = 0; i != n; ++i) bam_close(fp[i]);
bam_close(fpout);
free(fp); free(heap);
}
int bam_merge(int argc, char *argv[])
{
int c, is_by_qname = 0;
- while ((c = getopt(argc, argv, "n")) >= 0) {
+ char *fn_headers = NULL;
+
+ while ((c = getopt(argc, argv, "h:n")) >= 0) {
switch (c) {
+ case 'h': fn_headers = strdup(optarg); break;
case 'n': is_by_qname = 1; 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 [-n] [-h inh.sam] <out.bam> <in1.bam> <in2.bam> [...]\n\n");
+ fprintf(stderr, "Options: -n sort by read names\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);
+ bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1);
+ free(fn_headers);
return 0;
}
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);
free(fnout);
for (i = 0; i < n; ++i) {
unlink(fns[i]);
projects / samtools.git / blobdiff