fixed a few bugs in the indel caller. Probably there are more.

[samtools.git] / bam_sort.c

diff --git a/bam_sort.c b/bam_sort.c
index 4745be6cbf003c6a46a7882762c740c25493f932..76ab793196ca76fc5a63d619e230cf0fb5f59f1e 100644 (file)
--- 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;