Imported Upstream version 0.1.9

[samtools.git] / sam_view.c

diff --git a/sam_view.c b/sam_view.c
index 3b10e2e5372e98a2b9ebda4bd5791dc1b837a20f..d0fdad25445508e90052970a90de92e1f0f61ae5 100644 (file)
--- 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
        }