* samtools-0.1.6-18 (r493)

[samtools.git] / bam.c

diff --git a/bam.c b/bam.c
index 837b956c8e879734550bdbb7b0dfeb034dcd91ad..ee7642b3434248c9b44ef918435f150f101cae00 100644 (file)
--- a/bam.c
+++ b/bam.c
@@ -5,6 +5,7 @@
 #include "bam.h"
 #include "bam_endian.h"
 #include "kstring.h"
+#include "sam_header.h"
 
 int bam_is_be = 0;
 char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
@@ -59,10 +60,9 @@ void bam_header_destroy(bam_header_t *header)
                free(header->target_len);
        }
        free(header->text);
-#ifndef BAM_NO_HASH
-       if (header->rg2lib) bam_strmap_destroy(header->rg2lib);
+       if (header->dict) sam_header_free(header->dict);
+       if (header->rg2lib) sam_tbl_destroy(header->rg2lib);
        bam_destroy_header_hash(header);
-#endif
        free(header);
 }
 
@@ -291,3 +291,13 @@ void bam_view1(const bam_header_t *header, const bam1_t *b)
        printf("%s\n", s);
        free(s);
 }
+
+// FIXME: we should also check the LB tag associated with each alignment
+const char *bam_get_library(bam_header_t *h, const bam1_t *b)
+{
+       const uint8_t *rg;
+       if (h->dict == 0) h->dict = sam_header_parse2(h->text);
+       if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB");
+       rg = bam_aux_get(b, "RG");
+       return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1));
+}