X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam2bcf.c;h=dec3305340f689a100d29dc4f9b5998e7692c6d4;hp=088635c0b04a549b762d1a3b28efad82f4bb5c80;hb=9a36c994ed991f79cc191ece6cbc5f1bf6410da2;hpb=016b50ab60e879a0b8f81cb76ce11ea360a03d4a diff --git a/bam2bcf.c b/bam2bcf.c index 088635c..dec3305 100644 --- 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; } @@ -36,6 +39,7 @@ 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) { @@ -61,7 +65,8 @@ 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 +80,7 @@ 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; @@ -90,9 +95,92 @@ 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; imvd[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; i2*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(stderr,"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(stderr,"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]; @@ -140,8 +228,8 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, x = call->n_alleles * (call->n_alleles + 1) / 2; // get the possible genotypes for (i = z = 0; i < call->n_alleles; ++i) - for (j = i; j < call->n_alleles; ++j) - g[z++] = call->a[i] * 5 + call->a[j]; + for (j = 0; j <= i; ++j) + g[z++] = call->a[j] * 5 + call->a[i]; for (i = 0; i < n; ++i) { uint8_t *PL = call->PL + x * i; const bcf_callret1_t *r = calls + i; @@ -166,6 +254,9 @@ 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; } @@ -219,6 +310,10 @@ 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); @@ -232,7 +327,7 @@ 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; - uint8_t *sp = is_SP? b->gi[2].data : 0; + int32_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;