int bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem)
{
int ret;
char *fnout = calloc(strlen(prefix) + 4 + 1, 1);
sprintf(fnout, "%s.bam", prefix);
ret = bam_sort_core_ext(is_by_qname, fn, prefix, fnout, "wb", max_mem, 0);
free(fnout);
return ret;
}
int bam_sort(int argc, char *argv[])
{
size_t max_mem = 500000000;
int c, is_by_qname = 0, is_stdout = 0;
while ((c = getopt(argc, argv, "nom:")) >= 0) {
switch (c) {
case 'o': is_stdout = 1; break;
case 'n': is_by_qname = 1; break;
case 'm': max_mem = atol(optarg); break;
}
}
if (optind + 2 > argc) {
fprintf(stderr, "Usage: samtools sort [-on] [-m <maxMem>] <in.bam> <out.prefix>\n");
return 1;
}
bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout);
return 0;
}
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, level = -1, sort_type = 0;
while ((c = getopt(argc, argv, "nom:@:l:s:")) >= 0) {
switch (c) {
case 'o': is_stdout = 1; break;
case 'n': is_by_qname = 1; break;
case 'm': {
char *q;
max_mem = strtol(optarg, &q, 0);
if (*q == 'k' || *q == 'K') max_mem <<= 10;
else if (*q == 'm' || *q == 'M') max_mem <<= 20;
else if (*q == 'g' || *q == 'G') max_mem <<= 30;
break;
}
case '@': n_threads = atoi(optarg); break;
case 'l': level = atoi(optarg); break;
case 's': sort_type = atoi(optarg); break;
}
}
if (optind + 2 > argc) {
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, " -s sorting algorithm type [0]\n");
fprintf(stderr, " 0: mergesort\n");
fprintf(stderr, " 1: introsort\n");
fprintf(stderr, " 2: combsort\n");
fprintf(stderr, " 3: heapsort\n");
#ifndef _PBGZF_USE
fprintf(stderr, " -@ INT number of sorting and compression threads [1]\n");
#else
fprintf(stderr, " -@ INT number of sorting threads [1]\n");
#endif
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, sort_type);
return 0;
}
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, level = -1, full_path = 0;
while ((c = getopt(argc, argv, "fnom:@:l:")) >= 0) {
switch (c) {
case 'f': full_path = 1; break;
case 'o': is_stdout = 1; break;
case 'n': is_by_qname = 1; break;
case 'm': {
char *q;
max_mem = strtol(optarg, &q, 0);
if (*q == 'k' || *q == 'K') max_mem <<= 10;
else if (*q == 'm' || *q == 'M') max_mem <<= 20;
else if (*q == 'g' || *q == 'G') max_mem <<= 30;
break;
}
case '@': n_threads = atoi(optarg); break;
case 'l': level = atoi(optarg); break;
}
}
if (optind + 2 > argc) {
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, " -f use <out.prefix> as full file name instead of prefix\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, full_path);
return 0;
}
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, -1, 0);
}
int bam_sort(int argc, char *argv[])
{
size_t max_mem = 768<<20; // 512MB
int c, i, modern, nargs, is_by_qname = 0, is_stdout = 0, ret = EXIT_SUCCESS, n_threads = 0, level = -1, full_path = 0;
char *fnout = "-", *fmtout = NULL, modeout[12], *tmpprefix = NULL;
kstring_t fnout_buffer = { 0, 0, NULL };
modern = 0;
for (i = 1; i < argc; ++i)
if (argv[i][0] == '-' && strpbrk(argv[i], "OT")) { modern = 1; break; }
while ((c = getopt(argc, argv, modern? "l:m:no:O:T:@:" : "fnom:@:l:")) >= 0) {
switch (c) {
case 'f': full_path = 1; break;
case 'o': if (modern) fnout = optarg; else is_stdout = 1; break;
case 'n': is_by_qname = 1; break;
case 'm': {
char *q;
max_mem = strtol(optarg, &q, 0);
if (*q == 'k' || *q == 'K') max_mem <<= 10;
else if (*q == 'm' || *q == 'M') max_mem <<= 20;
else if (*q == 'g' || *q == 'G') max_mem <<= 30;
break;
}
case 'O': fmtout = optarg; break;
case 'T': tmpprefix = optarg; break;
case '@': n_threads = atoi(optarg); break;
case 'l': level = atoi(optarg); break;
default: return sort_usage(pysamerr, EXIT_FAILURE);
}
}
nargs = argc - optind;
if (argc == 1)
return sort_usage(stdout, EXIT_SUCCESS);
else if (modern? (nargs > 1) : (nargs != 2))
return sort_usage(pysamerr, EXIT_FAILURE);
if (!modern) {
fmtout = "bam";
if (is_stdout) fnout = "-";
else if (full_path) fnout = argv[optind+1];
else {
ksprintf(&fnout_buffer, "%s.%s", argv[optind+1], fmtout);
fnout = fnout_buffer.s;
}
tmpprefix = argv[optind+1];
}
strcpy(modeout, "w");
if (sam_open_mode(&modeout[1], fnout, fmtout) < 0) {
if (fmtout) fprintf(pysamerr, "[bam_sort] can't parse output format \"%s\"\n", fmtout);
else fprintf(pysamerr, "[bam_sort] can't determine output format\n");
ret = EXIT_FAILURE;
goto sort_end;
}
if (level >= 0) sprintf(strchr(modeout, '\0'), "%d", level < 9? level : 9);
if (tmpprefix == NULL) {
fprintf(pysamerr, "[bam_sort] no prefix specified for temporary files (use -T option)\n");
ret = EXIT_FAILURE;
goto sort_end;
}
if (bam_sort_core_ext(is_by_qname, (nargs > 0)? argv[optind] : "-", tmpprefix, fnout, modeout, max_mem, n_threads) < 0) ret = EXIT_FAILURE;
sort_end:
free(fnout_buffer.s);
return ret;
}
