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r389: return non-zero upon errors

This commit is contained in:
Heng Li 2013-04-27 10:08:01 -04:00
parent 19cb7cd7ed
commit 1a2bd2cf91
3 changed files with 13 additions and 5 deletions
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10
fastmap.c
View File

@ -90,9 +90,12 @@ int main_mem(int argc, char *argv[])
bwa_fill_scmat(opt->a, opt->b, opt->mat); bwa_fill_scmat(opt->a, opt->b, opt->mat);
if ((idx = bwa_idx_load(argv[optind], BWA_IDX_ALL)) == 0) return 1; // FIXME: memory leak if ((idx = bwa_idx_load(argv[optind], BWA_IDX_ALL)) == 0) return 1; // FIXME: memory leak
bwa_print_sam_hdr(idx->bns, rg_line);
ko = kopen(argv[optind + 1], &fd); ko = kopen(argv[optind + 1], &fd);
if (ko == 0) {
if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] fail to open file `%s'.\n", __func__, argv[optind + 1]);
return 1;
}
fp = gzdopen(fd, "r"); fp = gzdopen(fd, "r");
ks = kseq_init(fp); ks = kseq_init(fp);
if (optind + 2 < argc) { if (optind + 2 < argc) {
@ -101,11 +104,16 @@ int main_mem(int argc, char *argv[])
fprintf(stderr, "[W::%s] when '-p' is in use, the second query file will be ignored.\n", __func__); fprintf(stderr, "[W::%s] when '-p' is in use, the second query file will be ignored.\n", __func__);
} else { } else {
ko2 = kopen(argv[optind + 2], &fd2); ko2 = kopen(argv[optind + 2], &fd2);
if (ko2 == 0) {
if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] fail to open file `%s'.\n", __func__, argv[optind + 2]);
return 1;
}
fp2 = gzdopen(fd2, "r"); fp2 = gzdopen(fd2, "r");
ks2 = kseq_init(fp2); ks2 = kseq_init(fp2);
opt->flag |= MEM_F_PE; opt->flag |= MEM_F_PE;
} }
} }
bwa_print_sam_hdr(idx->bns, rg_line);
while ((seqs = bseq_read(opt->chunk_size * opt->n_threads, &n, ks, ks2)) != 0) { while ((seqs = bseq_read(opt->chunk_size * opt->n_threads, &n, ks, ks2)) != 0) {
int64_t size = 0; int64_t size = 0;
if ((opt->flag & MEM_F_PE) && (n&1) == 1) { if ((opt->flag & MEM_F_PE) && (n&1) == 1) {

4
kopen.c
View File

@ -292,14 +292,14 @@ void *kopen(const char *fn, int *_fd)
#else #else
*_fd = open(fn, O_RDONLY); *_fd = open(fn, O_RDONLY);
#endif #endif
if (*_fd) { if (*_fd >= 0) {
aux = calloc(1, sizeof(koaux_t)); aux = calloc(1, sizeof(koaux_t));
aux->type = KO_FILE; aux->type = KO_FILE;
aux->fd = *_fd; aux->fd = *_fd;
} }
} }
} }
*_fd = aux->fd; if (aux) *_fd = aux->fd;
return aux; return aux;
} }

4
main.c
View File

@ -3,7 +3,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.4-r388-beta" #define PACKAGE_VERSION "0.7.4-r389-beta"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);
@ -92,5 +92,5 @@ int main(int argc, char *argv[])
fprintf(stderr, " %s", argv[i]); fprintf(stderr, " %s", argv[i]);
fprintf(stderr, "\n[%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - t_real, cputime()); fprintf(stderr, "\n[%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - t_real, cputime());
} }
return 0; return ret;
} }