@discussion Padding information may NOT correctly maintained. This
function is NOT thread safe.
*/
-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 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;
}
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);
+ 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, n_threads = 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;
}
}
return 1;
}
}
- if (bam_merge_core2(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg, n_threads) < 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;
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, int n_threads)
+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 ret, i, extra_mem, n_files = 0;
size_t mem, max_k, k, max_mem;
else sprintf(fnout, "%s.bam", prefix);
// 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, "w", k, buf, header, n_threads);
+ 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);
fns[i] = (char*)calloc(strlen(prefix) + 20, 1);
sprintf(fns[i], "%s.%.4d.bam", prefix, i);
}
- bam_merge_core2(is_by_qname, fnout, 0, n_files, fns, 0, 0, n_threads);
+ 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]);
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, 0);
+ bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0, 0, -1);
}
int bam_sort(int argc, char *argv[])
{
size_t max_mem = 768<<20; // 512MB
- int c, is_by_qname = 0, is_stdout = 0, n_threads = 0;
- while ((c = getopt(argc, argv, "nom:@:")) >= 0) {
+ int c, is_by_qname = 0, is_stdout = 0, n_threads = 0, level = -1;
+ while ((c = getopt(argc, argv, "nom:@:l:")) >= 0) {
switch (c) {
case 'o': is_stdout = 1; break;
case 'n': is_by_qname = 1; break;
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=1G] <in.bam> <out.prefix>\n");
return 1;
}
- bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads);
+ bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads, level);
return 0;
}