Ensure exit status of 1 if given invalid options or index files are n…

…ot 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.

bwape.c

@@ -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);

bwase.c

@@ -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);

bwtaln.c

@@ -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);

bwtsw2_main.c

@@ -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);

fastmap.c

@@ -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);

pemerge.c

@@ -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;