* samtools-0.1.5-34 (r451)

[samtools.git] / bam_sort.c

diff --git a/bam_sort.c b/bam_sort.c
index c43e56f356a5578d0a2365ddba5708826fb96975..a2d3d09473730715b78f38d6abb2b0123589daca 100644 (file)
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -49,23 +49,44 @@ static inline int heap_lt(const heap1_t a, const heap1_t b)
 
 KSORT_INIT(heap, heap1_t, heap_lt)
 
+static void swap_header_text(bam_header_t *h1, bam_header_t *h2)
+{
+       int tempi;
+       char *temps;
+       tempi = h1->l_text, h1->l_text = h2->l_text, h2->l_text = tempi;
+       temps = h1->text, h1->text = h2->text, h2->text = temps;
+}
+
 /*!
   @abstract    Merge multiple sorted BAM.
   @param  is_by_qname whether to sort by query name
   @param  out  output BAM file name
+  @param  headers  name of SAM file from which to copy '@' header lines,
+                   or NULL to copy them from the first file to be merged
   @param  n    number of files to be merged
   @param  fn   names of files to be merged
 
   @discussion Padding information may NOT correctly maintained. This
   function is NOT thread safe.
  */
-void bam_merge_core(int by_qname, const char *out, int n, char * const *fn)
+void bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn)
 {
        bamFile fpout, *fp;
        heap1_t *heap;
        bam_header_t *hout = 0;
+       bam_header_t *hheaders = NULL;
        int i, j;
 
+       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);
+               }
+       }
+
        g_is_by_qname = by_qname;
        fp = (bamFile*)calloc(n, sizeof(bamFile));
        heap = (heap1_t*)calloc(n, sizeof(heap1_t));
@@ -74,8 +95,24 @@ void bam_merge_core(int by_qname, const char *out, int n, char * const *fn)
                bam_header_t *hin;
                assert(fp[i] = bam_open(fn[i], "r"));
                hin = bam_header_read(fp[i]);
-               if (i == 0) hout = hin;
-               else { // validate multiple baf
+               if (i == 0) { // the first SAM
+                       hout = hin;
+                       if (hheaders) {
+                               // If the text headers to be swapped in include any @SQ headers,
+                               // 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)
+                                               fprintf(stderr, "[bam_merge_core] number of @SQ headers in `%s' differs from number of target sequences", headers);
+                                       for (j = 0; j < hout->n_targets; ++j)
+                                               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);
+                               }
+                               swap_header_text(hout, hheaders);
+                               bam_header_destroy(hheaders);
+                               hheaders = NULL;
+                       }
+               } 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);
@@ -86,9 +123,6 @@ void bam_merge_core(int by_qname, const char *out, int n, char * const *fn)
                                                        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);
                }
@@ -125,16 +159,26 @@ void bam_merge_core(int by_qname, const char *out, int n, char * const *fn)
 int bam_merge(int argc, char *argv[])
 {
        int c, is_by_qname = 0;
-       while ((c = getopt(argc, argv, "n")) >= 0) {
+       char *fn_headers = NULL;
+
+       while ((c = getopt(argc, argv, "h:n")) >= 0) {
                switch (c) {
+               case 'h': fn_headers = strdup(optarg); break;
                case 'n': is_by_qname = 1; break;
                }
        }
        if (optind + 2 >= argc) {
-               fprintf(stderr, "Usage: samtools merge [-n] <out.bam> <in1.bam> <in2.bam> [...]\n");
+               fprintf(stderr, "\n");
+               fprintf(stderr, "Usage:   samtools merge [-n] [-h inh.sam] <out.bam> <in1.bam> <in2.bam> [...]\n\n");
+               fprintf(stderr, "Options: -n       sort by read names\n");
+               fprintf(stderr, "         -h FILE  copy the header in FILE to <out.bam> [in1.bam]\n\n");
+               fprintf(stderr, "Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users\n");
+               fprintf(stderr, "      must provide the correct header with -h, or uses Picard which properly maintains\n");
+               fprintf(stderr, "      the header dictionary in merging.\n\n");
                return 1;
        }
-       bam_merge_core(is_by_qname, argv[optind], argc - optind - 1, argv + optind + 1);
+       bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1);
+       free(fn_headers);
        return 0;
 }
 
@@ -220,10 +264,10 @@ void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t m
                        fns[i] = (char*)calloc(strlen(prefix) + 20, 1);
                        sprintf(fns[i], "%s.%.4d.bam", prefix, i);
                }
-               bam_merge_core(is_by_qname, fnout, n, fns);
+               bam_merge_core(is_by_qname, fnout, 0, n, fns);
                free(fnout);
                for (i = 0; i < n; ++i) {
-//                     unlink(fns[i]);
+                       unlink(fns[i]);
                        free(fns[i]);
                }
                free(fns);