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Ensure exit status of 1 if given invalid options or index files are not found. 

Added missing default cases in option scanning.
Ensure exit value is 1 if bwa_idx_load or bwa_idx_infer_prefix fail.
These changes extend the previous one, which only fixed the mem aligner.
This commit is contained in:
Rob Davies 2013-04-29 13:58:28 +01:00
parent e88529687f
commit 0aa7e0a402
6 changed files with 9 additions and 5 deletions
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2
bwape.c
View File

@ -765,7 +765,7 @@ int bwa_sai2sam_pe(int argc, char *argv[])
}
if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
fprintf(stderr, "[%s] fail to locate the index\n", __func__);
return 0;
return 1;
}
bwa_sai2sam_pe_core(prefix, argv + optind + 1, argv + optind+3, popt, rg_line);
free(prefix); free(popt);

2
bwase.c
View File

@ -611,7 +611,7 @@ int bwa_sai2sam_se(int argc, char *argv[])
}
if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
fprintf(stderr, "[%s] fail to locate the index\n", __func__);
return 0;
return 1;
}
bwa_sai2sam_se_core(prefix, argv[optind+1], argv[optind+2], n_occ, rg_line);
free(prefix);

2
bwtaln.c
View File

@ -306,7 +306,7 @@ int bwa_aln(int argc, char *argv[])
if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
fprintf(stderr, "[%s] fail to locate the index\n", __func__);
free(opt);
return 0;
return 1;
}
bwa_aln_core(prefix, argv[optind+1], opt);
free(opt); free(prefix);

3
bwtsw2_main.c
View File

@ -37,6 +37,7 @@ int bwa_bwtsw2(int argc, char *argv[])
case 'S': opt->skip_sw = 1; break;
case 'C': opt->cpy_cmt = 1; break;
case 'G': opt->max_chain_gap = atoi(optarg); break;
default: return 1;
}
}
opt->qr = opt->q + opt->r;
@ -79,7 +80,7 @@ int bwa_bwtsw2(int argc, char *argv[])
opt->t *= opt->a;
opt->coef *= opt->a;
if ((idx = bwa_idx_load(argv[optind], BWA_IDX_BWT|BWA_IDX_BNS)) == 0) return 0;
if ((idx = bwa_idx_load(argv[optind], BWA_IDX_BWT|BWA_IDX_BNS)) == 0) return 1;
bsw2_aln(opt, idx->bns, idx->bwt, argv[optind+1], optind+2 < argc? argv[optind+2] : 0);
bwa_idx_destroy(idx);
free(opt);

4
fastmap.c
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@ -52,6 +52,7 @@ int main_mem(int argc, char *argv[])
else if (c == 'R') {
if ((rg_line = bwa_set_rg(optarg)) == 0) return 1; // FIXME: memory leak
} else if (c == 's') opt->split_width = atoi(optarg);
else return 1;
}
if (opt->n_threads < 1) opt->n_threads = 1;
if (optind + 1 >= argc) {
@ -164,6 +165,7 @@ int main_fastmap(int argc, char *argv[])
case 'p': print_seq = 1; break;
case 'w': min_iwidth = atoi(optarg); break;
case 'l': min_len = atoi(optarg); break;
default: return 1;
}
}
if (optind + 1 >= argc) {
@ -173,7 +175,7 @@ int main_fastmap(int argc, char *argv[])
fp = xzopen(argv[optind + 1], "r");
seq = kseq_init(fp);
idx = bwa_idx_load(argv[optind], BWA_IDX_BWT|BWA_IDX_BNS);
if ((idx = bwa_idx_load(argv[optind], BWA_IDX_BWT|BWA_IDX_BNS)) == 0) return 1;
itr = smem_itr_init(idx->bwt);
while (kseq_read(seq) >= 0) {
err_printf("SQ\t%s\t%ld", seq->name.s, seq->seq.l);

1
pemerge.c
View File

@ -226,6 +226,7 @@ int main_pemerge(int argc, char *argv[])
else if (c == 'Q') opt->q_thres = atoi(optarg);
else if (c == 't') opt->n_threads = atoi(optarg);
else if (c == 'T') min_ovlp = atoi(optarg);
else return 1;
}
if (flag == 0) flag = 3;
opt->flag = flag;