Updated samtools to 0.1.19

[rsem.git] / sam / bam_md.c

diff --git a/sam/bam_md.c b/sam/bam_md.c
index d42aa8fc971fa627ccf34a781f0432214ac6f8e0..ce40a121f1d05f6de6b7d8d73624700ff303d5fc 100644 (file)
--- a/sam/bam_md.c
+++ b/sam/bam_md.c
@@ -188,7 +188,7 @@ int bam_cap_mapQ(bam1_t *b, char *ref, int thres)
 
 int bam_prob_realn_core(bam1_t *b, const char *ref, int flag)
 {
-       int k, i, bw, x, y, yb, ye, xb, xe, apply_baq = flag&1, extend_baq = flag>>1&1;
+       int k, i, bw, x, y, yb, ye, xb, xe, apply_baq = flag&1, extend_baq = flag>>1&1, redo_baq = flag&4;
        uint32_t *cigar = bam1_cigar(b);
        bam1_core_t *c = &b->core;
        kpa_par_t conf = kpa_par_def;
@@ -197,6 +197,11 @@ int bam_prob_realn_core(bam1_t *b, const char *ref, int flag)
        // test if BQ or ZQ is present
        if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq;
        if ((zq = bam_aux_get(b, "ZQ")) != 0 && *zq == 'Z') ++zq;
+       if (bq && redo_baq)
+       {
+           bam_aux_del(b, bq-1);
+           bq = 0;
+       }
        if (bq && zq) { // remove the ZQ tag
                bam_aux_del(b, zq-1);
                zq = 0;