* This revision is SERIOUSLY BUGGY. Please NOT use it.

[samtools.git] / bam.c

diff --git a/bam.c b/bam.c
index f6e05ff4285ef6743387e33942b91c91bf0e85fc..8b517565026f276d860f91634789ec8fa2f36195 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";
@@ -13,28 +14,6 @@ char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
  * CIGAR related routines *
  **************************/
 
-int bam_segreg(int32_t pos, const bam1_core_t *c, const uint32_t *cigar, bam_segreg_t *reg)
-{
-       unsigned k;
-       int32_t x = c->pos, y = 0;
-       int state = 0;
-       for (k = 0; k < c->n_cigar; ++k) {
-               int op = cigar[k] & BAM_CIGAR_MASK; // operation
-               int l = cigar[k] >> BAM_CIGAR_SHIFT; // length
-               if (state == 0 && (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CINS) && x + l > pos) {
-                       reg->tbeg = x; reg->qbeg = y; reg->cbeg = k;
-                       state = 1;
-               }
-               if (op == BAM_CMATCH) { x += l; y += l; }
-               else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l;
-               else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
-               if (state == 1 && (op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP || op == BAM_CREF_SKIP || k == c->n_cigar - 1)) {
-                       reg->tend = x; reg->qend = y; reg->cend = k;
-               }
-       }
-       return state? 0 : -1;
-}
-
 uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar)
 {
        uint32_t k, end;
@@ -81,10 +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);
 }
 
@@ -313,3 +291,10 @@ void bam_view1(const bam_header_t *header, const bam1_t *b)
        printf("%s\n", s);
        free(s);
 }
+
+const char *bam_get_library(const bam_header_t *header, const bam1_t *b)
+{
+       const uint8_t *rg;
+       rg = bam_aux_get(b, "RG");
+       return (rg == 0)? 0 : sam_tbl_get(header->rg2lib, (const char*)(rg + 1));
+}