Merge pull request #2 from daviesrob/0.5.10-mt_fixes

Ensure we exit 1 when given an invalid command-line option.
wtsi-npg · May 12, 2015 · b8267d8 · b8267d8
2 parents c3a60e8 + d242fa6
commit b8267d8
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diff --git a/bwtsw2_main.c b/bwtsw2_main.c
@@ -34,6 +34,7 @@ int bwa_bwtsw2(int argc, char *argv[])
 		case 'N': opt->t_seeds = atoi(optarg); break;
 		case 'H': opt->hard_clip = 1; break;
 		case 'f': xreopen(optarg, "w", stdout); break;
+		default: return 1;
 		}
 	}
 	opt->qr = opt->q + opt->r;

diff --git a/simple_dp.c b/simple_dp.c
@@ -138,6 +138,7 @@ int bwa_stdsw(int argc, char *argv[])
 		case 'f': g_strand |= 1; break;
 		case 'r': g_strand |= 2; break;
 		case 'p': g_aa = 1; break;
+		default: return 1;
 		}
 	}
 	if (g_strand == 0) g_strand = 3;