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");
*/
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;
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;
+ 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);