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");
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) {
*/
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);
}
}
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, level);