* samtools-0.1.6-12 (r478)

[samtools.git] / bam.c

diff --git a/bam.c b/bam.c
index 533250b95771d73d626a247ca58bc1c2a167fee6..837b956c8e879734550bdbb7b0dfeb034dcd91ad 100644 (file)
--- a/bam.c
+++ b/bam.c
@@ -13,34 +13,6 @@ char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
  * CIGAR related routines *
  **************************/
 
-int bam_tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int32_t *_tpos)
-{
-       int k, x = c->pos, y = 0, last_y = 0;
-       *_tpos = c->pos;
-       for (k = 0; k < c->n_cigar; ++k) {
-               int op = cigar[k] & BAM_CIGAR_MASK;
-               int l = cigar[k] >> BAM_CIGAR_SHIFT;
-               if (op == BAM_CMATCH) {
-                       if (c->pos > tpos) return y;
-                       if (x + l > tpos) {
-                               *_tpos = tpos;
-                               return y + (tpos - x);
-                       }
-                       x += l; y += l;
-                       last_y = y;
-               } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
-               else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
-                       if (x + l > tpos) {
-                               *_tpos = x;
-                               return y;
-                       }
-                       x += l;
-               }
-       }
-       *_tpos = x;
-       return last_y;
-}
-
 uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar)
 {
        uint32_t k, end;