fixed a typo in the VCF header

[samtools.git] / bam2bcf.c

diff --git a/bam2bcf.c b/bam2bcf.c
index 088635c0b04a549b762d1a3b28efad82f4bb5c80..98acb5dd2ff051eacb86f8efd72c00c370798617 100644 (file)
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -11,6 +11,7 @@ extern        void ks_introsort_uint32_t(size_t n, uint32_t a[]);
 #define CALL_ETA 0.03f
 #define CALL_MAX 256
 #define CALL_DEFTHETA 0.83f
+#define DEF_MAPQ 20
 
 #define CAP_DIST 25
 
@@ -23,6 +24,8 @@ bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
        bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100;
        bca->min_baseQ = min_baseQ;
        bca->e = errmod_init(1. - theta);
+       bca->min_frac = 0.002;
+       bca->min_support = 1;
        return bca;
 }
 
@@ -61,7 +64,8 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
                seqQ = is_indel? (p->aux>>8&0xff) : 99;
                if (q < bca->min_baseQ) continue;
                if (q > seqQ) q = seqQ;
-               mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ;
+               mapQ = p->b->core.qual < 255? p->b->core.qual : DEF_MAPQ; // special case for mapQ==255
+               mapQ = mapQ < bca->capQ? mapQ : bca->capQ;
                if (q > mapQ) q = mapQ;
                if (q > 63) q = 63;
                if (q < 4) q = 4;
@@ -75,7 +79,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
                }
                bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
                // collect annotations
-               r->qsum[b] += q;
+               if (b < 4) r->qsum[b] += q;
                ++r->anno[0<<2|is_diff<<1|bam1_strand(p->b)];
                min_dist = p->b->core.l_qseq - 1 - p->qpos;
                if (min_dist > p->qpos) min_dist = p->qpos;