int bam_mating(int argc, char *argv[])
{
bamFile in, out;
if (argc < 3) {
fprintf(stderr, "Usage: samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
return 1;
}
in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");
out = (strcmp(argv[2], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[2], "w");
bam_mating_core(in, out);
bam_close(in); bam_close(out);
return 0;
}
int bam_mating(int argc, char *argv[])
{
samFile *in, *out;
int c, remove_reads = 0, proper_pair_check = 1, add_ct = 0;
sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
char wmode[3] = {'w', 'b', 0};
static const struct option lopts[] = {
SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0),
{ NULL, 0, NULL, 0 }
};
// parse args
if (argc == 1) { usage(stdout); return 0; }
while ((c = getopt_long(argc, argv, "rpcO:", lopts, NULL)) >= 0) {
switch (c) {
case 'r': remove_reads = 1; break;
case 'p': proper_pair_check = 0; break;
case 'c': add_ct = 1; break;
default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
/* else fall-through */
case '?': usage(stderr); return 1;
}
}
if (optind+1 >= argc) { usage(stderr); return 1; }
// init
if ((in = sam_open_format(argv[optind], "rb", &ga.in)) == NULL) {
fprintf(stderr, "[bam_mating] cannot open input file\n");
return 1;
}
sam_open_mode(wmode+1, argv[optind+1], NULL);
if ((out = sam_open_format(argv[optind+1], wmode, &ga.out)) == NULL) {
fprintf(stderr, "[bam_mating] cannot open output file\n");
return 1;
}
// run
bam_mating_core(in, out, remove_reads, proper_pair_check, add_ct);
// cleanup
sam_close(in); sam_close(out);
sam_global_args_free(&ga);
return 0;
}
int bam_mating(int argc, char *argv[])
{
bamFile in, out;
int c, remove_reads=0;
while ((c = getopt(argc, argv, "r")) >= 0) {
switch (c) {
case 'r':
remove_reads=1;
break;
}
}
if (optind+1 >= argc) usage();
in = (strcmp(argv[optind], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[optind], "r");
out = (strcmp(argv[optind+1], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[optind+1], "w");
bam_mating_core(in, out, remove_reads);
bam_close(in);
bam_close(out);
return 0;
}
int bam_mating(int argc, char *argv[])
{
htsThreadPool p = {NULL, 0};
samFile *in = NULL, *out = NULL;
int c, remove_reads = 0, proper_pair_check = 1, add_ct = 0, res = 1, mate_score = 0;
sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
char wmode[3] = {'w', 'b', 0};
static const struct option lopts[] = {
SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'),
{ NULL, 0, NULL, 0 }
};
// parse args
if (argc == 1) { usage(stdout); return 0; }
while ((c = getopt_long(argc, argv, "rpcmO:@:", lopts, NULL)) >= 0) {
switch (c) {
case 'r': remove_reads = 1; break;
case 'p': proper_pair_check = 0; break;
case 'c': add_ct = 1; break;
case 'm': mate_score = 1; break;
default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
/* else fall-through */
case '?': usage(stderr); goto fail;
}
}
if (optind+1 >= argc) { usage(stderr); goto fail; }
// init
if ((in = sam_open_format(argv[optind], "rb", &ga.in)) == NULL) {
print_error_errno("fixmate", "cannot open input file");
goto fail;
}
sam_open_mode(wmode+1, argv[optind+1], NULL);
if ((out = sam_open_format(argv[optind+1], wmode, &ga.out)) == NULL) {
print_error_errno("fixmate", "cannot open output file");
goto fail;
}
if (ga.nthreads > 0) {
if (!(p.pool = hts_tpool_init(ga.nthreads))) {
fprintf(stderr, "Error creating thread pool\n");
goto fail;
}
hts_set_opt(in, HTS_OPT_THREAD_POOL, &p);
hts_set_opt(out, HTS_OPT_THREAD_POOL, &p);
}
// run
res = bam_mating_core(in, out, remove_reads, proper_pair_check, add_ct, mate_score);
// cleanup
sam_close(in);
if (sam_close(out) < 0) {
fprintf(stderr, "[bam_mating] error while closing output file\n");
res = 1;
}
if (p.pool) hts_tpool_destroy(p.pool);
sam_global_args_free(&ga);
return res;
fail:
if (in) sam_close(in);
if (out) sam_close(out);
if (p.pool) hts_tpool_destroy(p.pool);
sam_global_args_free(&ga);
return 1;
}
