X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=sam_view.c;h=d0fdad25445508e90052970a90de92e1f0f61ae5;hp=3b10e2e5372e98a2b9ebda4bd5791dc1b837a20f;hb=85bb95099e58e20cc03456b7528248f7baed4db4;hpb=cb12a866906ec4ac644de0e658679261c82ab098

diff --git a/sam_view.c b/sam_view.c
index 3b10e2e..d0fdad2 100644
--- a/sam_view.c
+++ b/sam_view.c
@@ -124,15 +124,18 @@ int main_samview(int argc, char *argv[])
 	if (fn_list == 0 && fn_ref) fn_list = samfaipath(fn_ref);
 	// open file handlers
 	if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
-		fprintf(stderr, "[main_samview] fail to open file for reading.\n");
+		fprintf(stderr, "[main_samview] fail to open \"%s\" for reading.\n", argv[optind]);
+		ret = 1;
 		goto view_end;
 	}
 	if (in->header == 0) {
-		fprintf(stderr, "[main_samview] fail to read the header.\n");
+		fprintf(stderr, "[main_samview] fail to read the header from \"%s\".\n", argv[optind]);
+		ret = 1;
 		goto view_end;
 	}
 	if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
-		fprintf(stderr, "[main_samview] fail to open file for writing.\n");
+		fprintf(stderr, "[main_samview] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
+		ret = 1;
 		goto view_end;
 	}
 	if (is_header_only) goto view_end; // no need to print alignments
@@ -146,7 +149,10 @@ int main_samview(int argc, char *argv[])
 				samwrite(out, b); // write the alignment to `out'
 			}
 		}
-		if (r < -1) fprintf(stderr, "[main_samview] truncated file.\n");
+		if (r < -1) {
+			fprintf(stderr, "[main_samview] truncated file.\n");
+			ret = 1;
+		}
 		bam_destroy1(b);
 	} else { // retrieve alignments in specified regions
 		int i;
@@ -161,10 +167,15 @@ int main_samview(int argc, char *argv[])
 			int tid, beg, end;
 			bam_parse_region(in->header, argv[i], &tid, &beg, &end); // parse a region in the format like `chr2:100-200'
 			if (tid < 0) { // reference name is not found
-				fprintf(stderr, "[main_samview] fail to get the reference name. Continue anyway.\n");
+				fprintf(stderr, "[main_samview] region \"%s\" specifies an unknown reference name. Continue anyway.\n", argv[i]);
 				continue;
 			}
-			bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func); // fetch alignments
+			// fetch alignments
+			if (bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func) < 0) {
+				fprintf(stderr, "[main_samview] retrieval of region \"%s\" failed due to truncated file or corrupt BAM index file\n", argv[i]);
+				ret = 1;
+				break;
+			}
 		}
 		bam_index_destroy(idx); // destroy the BAM index
 	}