added the phase command

[samtools.git] / bam_sort.c

diff --git a/bam_sort.c b/bam_sort.c
index e4cc02f899c5ae724463bf7acb18f8fb4826f771..38f15d655c253dc1f7e8cd50dd39c178c448f584 100644 (file)
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -170,12 +170,12 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
                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);
-                               return -1;
+                               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);
-                                       return -1;
+                                       if (!reg) return -1;
                                }
                }
 
@@ -222,8 +222,11 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
        ks_heapmake(heap, n, heap);
        while (heap->pos != HEAP_EMPTY) {
                bam1_t *b = heap->b;
-               if ((flag & MERGE_RG) && bam_aux_get(b, "RG") == 0)
+               if (flag & MERGE_RG) {
+                       uint8_t *rg = bam_aux_get(b, "RG");
+                       if (rg) bam_aux_del(b, rg);
                        bam_aux_append(b, "RG", 'Z', RG_len[heap->i] + 1, (uint8_t*)RG[heap->i]);
+               }
                bam_write1_core(fpout, &b->core, b->data_len, b->data);
                if ((j = bam_iter_read(fp[heap->i], iter[heap->i], b)) >= 0) {
                        heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)b->core.pos<<1 | bam1_strand(b);