X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_sort.c;h=7c5fbb2faf4e7cc5268cbf924550461979bb4a84;hb=8cc87acf088966330e253d44e67791696d74f35b;hp=68d15dc58f7cde597615a5d49aa988f7a65cd366;hpb=635998cfe030da5f3dbec42a6daa3ca82fa5c871;p=samtools.git

diff --git a/bam_sort.c b/bam_sort.c
index 68d15dc..7c5fbb2 100644
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -66,13 +66,17 @@ void bam_merge_core(int by_qname, const char *out, int n, char * const *fn)
 		else { // validate multiple baf
 			if (hout->n_targets != hin->n_targets) {
 				fprintf(stderr, "[bam_merge_core] file '%s' has different number of target sequences. Abort!\n", fn[i]);
-				abort();
+				exit(1);
 			}
 			for (j = 0; j < hout->n_targets; ++j) {
-				if (strcmp(hout->target_name[j], hin->target_name[j]) || hout->target_len[j] != hin->target_len[j]) {
-					fprintf(stderr, "[bam_merge_core] file '%s' has a different target sequence. Abort!\n", fn[i]);
-					abort();
+				if (strcmp(hout->target_name[j], hin->target_name[j])) {
+					fprintf(stderr, "[bam_merge_core] different target sequence name: '%s' != '%s' in file '%s'. Abort!\n",
+							hout->target_name[j], hin->target_name[j], fn[i]);
+					exit(1);
 				}
+				if (hout->target_len[j] != hin->target_len[j])
+					fprintf(stderr, "[bam_merge_core] different target sequence length: %d != %d in file '%s'. Continue.\n",
+							hout->target_len[j], hin->target_len[j], fn[i]);
 			}
 			bam_header_destroy(hin);
 		}
@@ -115,7 +119,7 @@ int bam_merge(int argc, char *argv[])
 		case 'n': is_by_qname = 1; break;
 		}
 	}
-	if (optind + 3 >= argc) {
+	if (optind + 2 >= argc) {
 		fprintf(stderr, "Usage: samtools merge [-n] <out.bam> <in1.bam> <in2.bam> [...]\n");
 		return 1;
 	}
@@ -221,7 +225,7 @@ int bam_sort(int argc, char *argv[])
 		}
 	}
 	if (optind + 2 > argc) {
-		fprintf(stderr, "Usage: samtools sort [-n] [-m <maxMem>] <in.baf> <out.prefix>\n");
+		fprintf(stderr, "Usage: samtools sort [-n] [-m <maxMem>] <in.bam> <out.prefix>\n");
 		return 1;
 	}
 	bam_sort_core(is_by_qname, argv[optind], argv[optind+1], max_mem);