* allow to set min base q

[samtools.git] / bam2bcf.c

diff --git a/bam2bcf.c b/bam2bcf.c
index d69c771da80ef14ed925e549548f988a766ae680..e64e3357c04d5cd61bc7ecdc3e6af6d0fd859182 100644 (file)
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -12,18 +12,19 @@ extern      void ks_introsort_uint32_t(size_t n, uint32_t a[]);
 #define CALL_DEFTHETA 0.85f
 
 struct __bcf_callaux_t {
-       int max_info, capQ;
+       int max_info, capQ, min_baseQ;
        double *fk;
        uint32_t *info;
 };
 
-bcf_callaux_t *bcf_call_init(double theta)
+bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
 {
        bcf_callaux_t *bca;
        int n;
        if (theta <= 0.) theta = CALL_DEFTHETA;
        bca = calloc(1, sizeof(bcf_callaux_t));
        bca->capQ = 60;
+       bca->min_baseQ = min_baseQ;
        bca->fk = calloc(CALL_MAX, sizeof(double));
        bca->fk[0] = 1.;
        for (n = 1; n < CALL_MAX; ++n)
@@ -89,6 +90,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf
                uint32_t q, x = 0, qq;
                if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue; // skip unmapped reads and deleted bases
                q = (uint32_t)bam1_qual(p->b)[p->qpos]; // base quality
+               if (q < bca->min_baseQ) continue;
                x |= (uint32_t)bam1_strand(p->b) << 18 | q << 8 | p->b->core.qual;
                if (p->b->core.qual < q) q = p->b->core.qual; // cap the overall quality at mapping quality
                x |= q << 24;
@@ -137,17 +139,9 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf
                        p[j*5+k] = p[k*5+j] = 3.01 * (aux.c[j] + aux.c[k]) + tmp;
                }
        }
-       return 0;
+       return r->depth;
 }
 
-/*
-  1) Find the top 2 bases (from esum[4]).
-
-  2) If the reference base is among the top 2, consider the locus is
-     potentially biallelic and set call->a[2] as -1; otherwise, the
-     locus is potentially triallelic. If the reference is ambiguous,
-     take the weakest call as the pseudo-reference.
- */
 int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call)
 {
        int ref4, i, j;