X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=inline;f=bam_sort.c;h=76ab793196ca76fc5a63d619e230cf0fb5f59f1e;hb=543a65c4e127aa3d6c143a6bd50e128201f25784;hp=4745be6cbf003c6a46a7882762c740c25493f932;hpb=be38544a72499e002328fdf72dc7e30598306366;p=samtools.git

diff --git a/bam_sort.c b/bam_sort.c
index 4745be6..76ab793 100644
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -1,6 +1,7 @@
 #include <stdlib.h>
 #include <ctype.h>
 #include <assert.h>
+#include <errno.h>
 #include <stdio.h>
 #include <string.h>
 #include <unistd.h>
@@ -89,11 +90,12 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
 	if (headers) {
 		tamFile fpheaders = sam_open(headers);
 		if (fpheaders == 0) {
-			fprintf(stderr, "[bam_merge_core] Cannot open file `%s'. Continue anyway.\n", headers);
-		} else {
-			hheaders = sam_header_read(fpheaders);
-			sam_close(fpheaders);
+			const char *message = strerror(errno);
+			fprintf(stderr, "[bam_merge_core] cannot open '%s': %s\n", headers, message);
+			return -1;
 		}
+		hheaders = sam_header_read(fpheaders);
+		sam_close(fpheaders);
 	}
 
 	g_is_by_qname = by_qname;
@@ -135,11 +137,15 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
 				// check that they are consistent with the existing binary list
 				// of reference information.
 				if (hheaders->n_targets > 0) {
-					if (hout->n_targets != hheaders->n_targets)
+					if (hout->n_targets != hheaders->n_targets) {
 						fprintf(stderr, "[bam_merge_core] number of @SQ headers in `%s' differs from number of target sequences", headers);
+						if (!reg) return -1;
+					}
 					for (j = 0; j < hout->n_targets; ++j)
-						if (strcmp(hout->target_name[j], hheaders->target_name[j]) != 0)
+						if (strcmp(hout->target_name[j], hheaders->target_name[j]) != 0) {
 							fprintf(stderr, "[bam_merge_core] @SQ header '%s' in '%s' differs from target sequence", hheaders->target_name[j], headers);
+							if (!reg) return -1;
+						}
 				}
 				swap_header_text(hout, hheaders);
 				bam_header_destroy(hheaders);
@@ -147,14 +153,13 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
 			}
 		} 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]);
-				exit(1);
-			}
-			for (j = 0; j < hout->n_targets; ++j) {
-				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);
+				fprintf(stderr, "[bam_merge_core] file '%s' has different number of target sequences. Continue anyway!\n", fn[i]);
+			} else {
+				for (j = 0; j < hout->n_targets; ++j) {
+					if (strcmp(hout->target_name[j], hin->target_name[j])) {
+						fprintf(stderr, "[bam_merge_core] different target sequence name: '%s' != '%s' in file '%s'. Continue anyway!\n",
+								hout->target_name[j], hin->target_name[j], fn[i]);
+					}
 				}
 			}
 			bam_header_destroy(hin);
@@ -229,7 +234,7 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
 
 int bam_merge(int argc, char *argv[])
 {
-	int c, is_by_qname = 0, flag = 0;
+	int c, is_by_qname = 0, flag = 0, ret = 0;
 	char *fn_headers = NULL, *reg = 0;
 
 	while ((c = getopt(argc, argv, "h:nruR:")) >= 0) {
@@ -254,10 +259,10 @@ int bam_merge(int argc, char *argv[])
 		fprintf(stderr, "      the header dictionary in merging.\n\n");
 		return 1;
 	}
-	bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg);
+	if (bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg) < 0) ret = 1;
 	free(reg);
 	free(fn_headers);
-	return 0;
+	return ret;
 }
 
 typedef bam1_t *bam1_p;