Imported Upstream version 0.1.11

[samtools.git] / bam_sort.c

diff --git a/bam_sort.c b/bam_sort.c
index 76ab793196ca76fc5a63d619e230cf0fb5f59f1e..01f7016dd9a35ef27cf4cc232d7529b25d67880b 100644 (file)
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -52,6 +52,14 @@ static inline int heap_lt(const heap1_t a, const heap1_t b)
 
 KSORT_INIT(heap, heap1_t, heap_lt)
 
+static void swap_header_targets(bam_header_t *h1, bam_header_t *h2)
+{
+       bam_header_t t;
+       t.n_targets = h1->n_targets, h1->n_targets = h2->n_targets, h2->n_targets = t.n_targets;
+       t.target_name = h1->target_name, h1->target_name = h2->target_name, h2->target_name = t.target_name;
+       t.target_len = h1->target_len, h1->target_len = h2->target_len, h2->target_len = t.target_len;
+}
+
 static void swap_header_text(bam_header_t *h1, bam_header_t *h2)
 {
        int tempi;
@@ -130,42 +138,51 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
                        return -1;
                }
                hin = bam_header_read(fp[i]);
-               if (i == 0) { // the first SAM
+               if (i == 0) { // the first BAM
                        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);
-                                               if (!reg) return -1;
-                                       }
-                                       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);
-                                                       if (!reg) return -1;
-                                               }
-                               }
-                               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. 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]);
-                                       }
+                       int min_n_targets = hout->n_targets;
+                       if (hin->n_targets < min_n_targets) min_n_targets = hin->n_targets;
+
+                       for (j = 0; j < min_n_targets; ++j)
+                               if (strcmp(hout->target_name[j], hin->target_name[j]) != 0) {
+                                       fprintf(stderr, "[bam_merge_core] different target sequence name: '%s' != '%s' in file '%s'\n",
+                                                       hout->target_name[j], hin->target_name[j], fn[i]);
+                                       return -1;
                                }
+
+                       // If this input file has additional target reference sequences,
+                       // add them to the headers to be output
+                       if (hin->n_targets > hout->n_targets) {
+                               swap_header_targets(hout, hin);
+                               // FIXME Possibly we should also create @SQ text headers
+                               // for the newly added reference sequences
                        }
+
                        bam_header_destroy(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\n", headers);
+                               if (!reg) return -1;
+                       }
+                       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\n", hheaders->target_name[j], headers);
+                                       if (!reg) return -1;
+                               }
+               }
+
+               swap_header_text(hout, hheaders);
+               bam_header_destroy(hheaders);
+       }
+
        if (reg) {
                int tid, beg, end;
                if (bam_parse_region(hout, reg, &tid, &beg, &end) < 0) {