Merge commit 'upstream/0.1.10'

[samtools.git] / sam.c

diff --git a/sam.c b/sam.c
index a74c557bad9aa83d274ea44bdfe1a16dfbc4d5a6..ecdee02dddb98a32d47a59e3154179356acecadf 100644 (file)
--- a/sam.c
+++ b/sam.c
@@ -12,7 +12,7 @@ bam_header_t *bam_header_dup(const bam_header_t *h0)
        int i;
        h = bam_header_init();
        *h = *h0;
-       h->hash = 0;
+       h->hash = h->dict = h->rg2lib = 0;
        h->text = (char*)calloc(h->l_text + 1, 1);
        memcpy(h->text, h0->text, h->l_text);
        h->target_len = (uint32_t*)calloc(h->n_targets, 4);
@@ -21,7 +21,6 @@ bam_header_t *bam_header_dup(const bam_header_t *h0)
                h->target_len[i] = h0->target_len[i];
                h->target_name[i] = strdup(h0->target_name[i]);
        }
-       if (h0->rg2lib) h->rg2lib = bam_strmap_dup(h0->rg2lib);
        return h;
 }
 static void append_header_text(bam_header_t *header, char* text, int len)
@@ -56,6 +55,7 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
                                if (aux) { // check if aux is present
                                        bam_header_t *textheader = fp->header;
                                        fp->header = sam_header_read2((const char*)aux);
+                                       if (fp->header == 0) goto open_err_ret;
                                        append_header_text(fp->header, textheader->text, textheader->l_text);
                                        bam_header_destroy(textheader);
                                }
@@ -63,7 +63,6 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
                                        fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
                        } else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
                }
-               sam_header_parse_rg(fp->header);
        } else if (mode[0] == 'w') { // write
                fp->header = bam_header_dup((const bam_header_t*)aux);
                if (mode[1] == 'b') { // binary