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_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;
}
}
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");
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;
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)))));
+ 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)
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;
+ int ret, i, n_files = 0;
size_t mem, max_k, k, max_mem;
bam_header_t *header;
bamFile fp;
char *fnout = 0;
if (n_threads < 2) n_threads = 1;
- extra_mem = sizeof(void*) + sizeof(void*) + (sizeof(bam1_t) - sizeof(bam1_core_t));
g_is_by_qname = is_by_qname;
max_k = k = 0; mem = 0;
max_mem = _max_mem * n_threads;
return;
}
header = bam_header_read(fp);
+ if (is_by_qname) change_SO(header, "queryname");
+ else change_SO(header, "coordinate");
// write sub files
for (;;) {
if (k == max_k) {
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 + extra_mem;
+ 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) {
n_files = sort_blocks(n_files, k, buf, prefix, header, n_threads);
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");
+ 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, " -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, n_threads);
+ bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads, level);
return 0;
}
projects / samtools.git / blobdiff