@discussion Padding information may NOT correctly maintained. This
function is NOT thread safe.
*/
-void bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn)
+void bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int add_RG)
{
bamFile fpout, *fp;
heap1_t *heap;
bam_header_t *hout = 0;
bam_header_t *hheaders = NULL;
- int i, j;
+ int i, j, *RG_len = 0;
uint64_t idx = 0;
+ char **RG = 0;
if (headers) {
tamFile fpheaders = sam_open(headers);
g_is_by_qname = by_qname;
fp = (bamFile*)calloc(n, sizeof(bamFile));
heap = (heap1_t*)calloc(n, sizeof(heap1_t));
+ // prepare RG tag
+ if (add_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;
ks_heapmake(heap, n, heap);
while (heap->pos != HEAP_EMPTY) {
bam1_t *b = heap->b;
+ if (add_RG && bam_aux_get(b, "RG") == 0)
+ 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);
ks_heapadjust(heap, 0, n, heap);
}
+ if (add_RG) {
+ for (i = 0; i != n; ++i) free(RG[i]);
+ free(RG); free(RG_len);
+ }
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;
+ int c, is_by_qname = 0, add_RG = 0;
char *fn_headers = NULL;
- while ((c = getopt(argc, argv, "h:n")) >= 0) {
+ while ((c = getopt(argc, argv, "h:nr")) >= 0) {
switch (c) {
+ case 'r': add_RG = 1; break;
case 'h': fn_headers = strdup(optarg); break;
case 'n': is_by_qname = 1; break;
}
}
if (optind + 2 >= argc) {
fprintf(stderr, "\n");
- fprintf(stderr, "Usage: samtools merge [-n] [-h inh.sam] <out.bam> <in1.bam> <in2.bam> [...]\n\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, " -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], fn_headers, argc - optind - 1, argv + optind + 1);
+ bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, add_RG);
free(fn_headers);
return 0;
}
mem += ret;
++k;
if (mem >= max_mem) {
- sort_blocks(n++, k, buf, prefix, header, is_stdout);
+ sort_blocks(n++, k, buf, prefix, header, 0);
mem = 0; k = 0;
}
}
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, is_stdout);
+ 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[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);
+ bam_merge_core(is_by_qname, fnout, 0, n, fns, 0);
free(fnout);
for (i = 0; i < n; ++i) {
unlink(fns[i]);