X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fbam2bcf.c.pysam.c;h=06f85998d432012ac9baa56fa2f8ded3ae68ec5e;hp=ece837ae71089cb2640d5401143a449d5eae5fed;hb=e1756c41e7a1d7cc01fb95e42df9dd04da2d2991;hpb=ca46ef4ba4a883c57cea62d5bf1bc021f1185109

diff --git a/samtools/bam2bcf.c.pysam.c b/samtools/bam2bcf.c.pysam.c
index ece837a..06f8599 100644
--- a/samtools/bam2bcf.c.pysam.c
+++ b/samtools/bam2bcf.c.pysam.c
@@ -41,7 +41,6 @@ void bcf_call_destroy(bcf_callaux_t *bca)
  * negative if we are looking at an indel. */
 int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r)
 {
-    static int *var_pos = NULL, nvar_pos = 0;
 	int i, n, ref4, is_indel, ori_depth = 0;
 	memset(r, 0, sizeof(bcf_callret1_t));
 	if (ref_base >= 0) {
@@ -97,92 +96,9 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
 	r->depth = n; r->ori_depth = ori_depth;
 	// glfgen
 	errmod_cal(bca->e, n, 5, bca->bases, r->p);
-
-    // Calculate the Variant Distance Bias (make it optional?)
-    if ( nvar_pos < _n ) {
-        nvar_pos = _n;
-        var_pos = realloc(var_pos,sizeof(int)*nvar_pos);
-    }
-    int alt_dp=0, read_len=0;
-    for (i=0; i<_n; i++) {
-        const bam_pileup1_t *p = pl + i;
-        if ( bam1_seqi(bam1_seq(p->b),p->qpos) == ref_base ) 
-            continue;
-
-        var_pos[alt_dp] = p->qpos;
-        if ( (bam1_cigar(p->b)[0]&BAM_CIGAR_MASK)==4 )
-            var_pos[alt_dp] -= bam1_cigar(p->b)[0]>>BAM_CIGAR_SHIFT;
-
-        alt_dp++;
-        read_len += p->b->core.l_qseq;
-    }
-    float mvd=0;
-    int j;
-    n=0;
-    for (i=0; i<alt_dp; i++) {
-        for (j=0; j<i; j++) {
-            mvd += abs(var_pos[i] - var_pos[j]);
-            n++;
-        }
-    }
-    r->mvd[0] = n ? mvd/n : 0;
-    r->mvd[1] = alt_dp;
-    r->mvd[2] = alt_dp ? read_len/alt_dp : 0;
-
 	return r->depth;
 }
 
-
-void calc_vdb(int n, const bcf_callret1_t *calls, bcf_call_t *call)
-{
-    // Variant distance bias. Samples merged by means of DP-weighted average.
-
-    float weight=0, tot_prob=0;
-
-    int i;
-    for (i=0; i<n; i++)
-    {
-        int mvd      = calls[i].mvd[0];
-        int dp       = calls[i].mvd[1];
-        int read_len = calls[i].mvd[2];
-
-        if ( dp<2 ) continue;
-
-        float prob = 0;
-        if ( dp==2 )
-        {
-            // Exact formula
-            prob = (mvd==0) ? 1.0/read_len : (read_len-mvd)*2.0/read_len/read_len;
-        }
-        else if ( dp==3 )
-        {
-            // Sin, quite accurate approximation
-            float mu = read_len/2.9;
-            prob = mvd>2*mu ? 0 : sin(mvd*3.14/2/mu) / (4*mu/3.14);
-        }
-        else
-        {
-            // Scaled gaussian curve, crude approximation, but behaves well. Using fixed depth for bigger depths.
-            if ( dp>5 )
-                dp = 5;
-            float sigma2 = (read_len/1.9/(dp+1)) * (read_len/1.9/(dp+1));
-            float norm   = 1.125*sqrt(2*3.14*sigma2);
-            float mu     = read_len/2.9;
-            if ( mvd < mu )
-                prob = exp(-(mvd-mu)*(mvd-mu)/2/sigma2)/norm;
-            else
-                prob = exp(-(mvd-mu)*(mvd-mu)/3.125/sigma2)/norm;
-        }
-
-        //fprintf(pysamerr,"dp=%d mvd=%d read_len=%d -> prob=%f\n", dp,mvd,read_len,prob);
-        tot_prob += prob*dp;
-        weight += dp;
-    }
-    tot_prob = weight ? tot_prob/weight : 1; 
-    //fprintf(pysamerr,"prob=%f\n", tot_prob);
-    call->vdb = tot_prob;
-}
-
 int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call)
 {
 	int ref4, i, j, qsum[4];
@@ -256,9 +172,6 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
 		call->ori_depth += calls[i].ori_depth;
 		for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j];
 	}
-
-    calc_vdb(n, calls, call);
-
 	return 0;
 }
 
@@ -312,10 +225,6 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc
 		if (i) kputc(',', &s);
 		kputw(bc->anno[i], &s);
 	}
-    if ( bc->vdb!=1 )
-    {
-        ksprintf(&s, ";VDB=%.4f", bc->vdb);
-    }
 	kputc('\0', &s);
 	// FMT
 	kputs("PL", &s);
@@ -329,7 +238,7 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc
 	memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n);
 	if (bcr) {
 		uint16_t *dp = (uint16_t*)b->gi[1].data;
-		int32_t *sp = is_SP? b->gi[2].data : 0;
+		uint8_t *sp = is_SP? b->gi[2].data : 0;
 		for (i = 0; i < bc->n; ++i) {
 			bcf_callret1_t *p = bcr + i;
 			dp[i] = p->depth < 0xffff? p->depth : 0xffff;