X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.c;h=340b10b8ff2ebfc1807af7f2c3b30b35a3dade3e;hb=941fbbbf695efff2c78765d8d0c415ae19b516a1;hp=de6a3ed367b90bea3a4fc7430c9f4b4fa5bf26e4;hpb=917ed8ca3a137ff2c2db887c0c72f3cce09f7df4;p=samtools.git

diff --git a/bam2bcf.c b/bam2bcf.c
index de6a3ed..340b10b 100644
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -1,5 +1,6 @@
 #include <math.h>
 #include <stdint.h>
+#include <assert.h>
 #include "bam.h"
 #include "kstring.h"
 #include "bam2bcf.h"
@@ -11,6 +12,7 @@ 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
 
@@ -20,23 +22,61 @@ bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
 	if (theta <= 0.) theta = CALL_DEFTHETA;
 	bca = calloc(1, sizeof(bcf_callaux_t));
 	bca->capQ = 60;
-	bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 80;
+	bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100;
 	bca->min_baseQ = min_baseQ;
 	bca->e = errmod_init(1. - theta);
-	return bca;
+	bca->min_frac = 0.002;
+	bca->min_support = 1;
+    bca->per_sample_flt = 0;
+    bca->npos = 100;
+    bca->ref_pos = calloc(bca->npos, sizeof(int));
+    bca->alt_pos = calloc(bca->npos, sizeof(int));
+ 	return bca;
+}
+
+
+static int get_position(const bam_pileup1_t *p, int *len)
+{
+    int icig, n_tot_bases = 0, iread = 0, edist = p->qpos + 1;
+    for (icig=0; icig<p->b->core.n_cigar; icig++) 
+    {
+        // Conversion from uint32_t to MIDNSHP
+        //  0123456
+        //  MIDNSHP
+        int cig  = bam1_cigar(p->b)[icig] & BAM_CIGAR_MASK;
+        int ncig = bam1_cigar(p->b)[icig] >> BAM_CIGAR_SHIFT;
+        if ( cig==0 )
+        {
+            n_tot_bases += ncig;
+            iread += ncig;
+        }
+        else if ( cig==1 )
+        {
+            n_tot_bases += ncig;
+            iread += ncig;
+        }
+        else if ( cig==4 )
+        {
+            iread += ncig;
+            if ( iread<=p->qpos ) edist -= ncig;
+        }
+    }
+    *len = n_tot_bases;
+    return edist;
 }
 
 void bcf_call_destroy(bcf_callaux_t *bca)
 {
 	if (bca == 0) return;
 	errmod_destroy(bca->e);
-	free(bca->bases); free(bca);
+    if (bca->npos) { free(bca->ref_pos); free(bca->alt_pos); bca->npos = 0; }
+	free(bca->bases); free(bca->inscns); free(bca);
 }
 /* ref_base is the 4-bit representation of the reference base. It is
  * 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)
 {
-	int i, n, ref4, is_indel;
+	int i, n, ref4, is_indel, ori_depth = 0;
 	memset(r, 0, sizeof(bcf_callret1_t));
 	if (ref_base >= 0) {
 		ref4 = bam_nt16_nt4_table[ref_base];
@@ -50,15 +90,18 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
 		bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
 	}
 	// fill the bases array
-	memset(r, 0, sizeof(bcf_callret1_t));
-	for (i = n = 0; i < _n; ++i) {
+	for (i = n = r->n_supp = 0; i < _n; ++i) {
 		const bam_pileup1_t *p = pl + i;
-		int q, b, mapQ, baseQ, is_diff, min_dist;
+		int q, b, mapQ, baseQ, is_diff, min_dist, seqQ;
 		// set base
 		if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue;
+		++ori_depth;
 		baseQ = q = is_indel? p->aux&0xff : (int)bam1_qual(p->b)[p->qpos]; // base/indel quality
+		seqQ = is_indel? (p->aux>>8&0xff) : 99;
 		if (q < bca->min_baseQ) continue;
-		mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ;
+		if (q > seqQ) q = seqQ;
+		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;
@@ -67,12 +110,13 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
 			b = bam_nt16_nt4_table[b? b : ref_base]; // b is the 2-bit base
 			is_diff = (ref4 < 4 && b == ref4)? 0 : 1;
 		} else {
-			b = p->aux>>8&0x3f;
+			b = p->aux>>16&0x3f;
 			is_diff = (b != 0);
 		}
+		if (is_diff) ++r->n_supp;
 		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;
@@ -83,14 +127,163 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
 		r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
 		r->anno[3<<2|is_diff<<1|0] += min_dist;
 		r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
+
+        // collect read positions for ReadPosBias
+        int len, pos = get_position(p, &len);
+        int epos = (double)pos/(len+1) * bca->npos;
+        if ( bam1_seqi(bam1_seq(p->b),p->qpos) == ref_base )
+            bca->ref_pos[epos]++;
+        else
+            bca->alt_pos[epos]++;
 	}
-	r->depth = n;
+	r->depth = n; r->ori_depth = ori_depth;
 	// glfgen
 	errmod_cal(bca->e, n, 5, bca->bases, r->p);
 	return r->depth;
 }
 
-int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call)
+double mann_whitney_1947(int n, int m, int U)
+{
+    if (U<0) return 0;
+    if (n==0||m==0) return U==0 ? 1 : 0;
+    return (double)n/(n+m)*mann_whitney_1947(n-1,m,U-m) + (double)m/(n+m)*mann_whitney_1947(n,m-1,U);
+}
+
+void calc_ReadPosBias(bcf_callaux_t *bca, bcf_call_t *call)
+{
+    int i, nref = 0, nalt = 0;
+    unsigned long int U = 0;
+    for (i=0; i<bca->npos; i++) 
+    {
+        nref += bca->ref_pos[i];
+        nalt += bca->alt_pos[i];
+        U += nref*bca->alt_pos[i];
+        bca->ref_pos[i] = 0;
+        bca->alt_pos[i] = 0;
+    }
+#if 0
+//todo
+    double var = 0, avg = (double)(nref+nalt)/bca->npos;
+    for (i=0; i<bca->npos; i++) 
+    {
+        double ediff = bca->ref_pos[i] + bca->alt_pos[i] - avg;
+        var += ediff*ediff;
+        bca->ref_pos[i] = 0;
+        bca->alt_pos[i] = 0;
+    }
+    call->read_pos.avg = avg;
+    call->read_pos.var = sqrt(var/bca->npos);
+    call->read_pos.dp  = nref+nalt;
+#endif
+    if ( !nref || !nalt )
+    {
+        call->read_pos_bias = -1;
+        return;
+    }
+
+    if ( nref>=8 || nalt>=8 )
+    {
+        // normal approximation
+        double mean = ((double)nref*nalt+1.0)/2.0;
+        double var2 = (double)nref*nalt*(nref+nalt+1.0)/12.0;
+        double z    = (U-mean)/sqrt(var2);
+        call->read_pos_bias = z;
+        //fprintf(stderr,"nref=%d  nalt=%d  U=%ld  mean=%e  var=%e  zval=%e\n", nref,nalt,U,mean,sqrt(var2),call->read_pos_bias);
+    }
+    else
+    {
+        double p = mann_whitney_1947(nalt,nref,U);
+        // biased form claimed by GATK to behave better empirically
+        // double var2 = (1.0+1.0/(nref+nalt+1.0))*(double)nref*nalt*(nref+nalt+1.0)/12.0;
+        double var2 = (double)nref*nalt*(nref+nalt+1.0)/12.0;
+        double z;
+        if ( p >= 1./sqrt(var2*2*M_PI) ) z = 0;   // equal to mean
+        else
+        {
+            if ( U >= nref*nalt/2. ) z = sqrt(-2*log(sqrt(var2*2*M_PI)*p));
+            else z = -sqrt(-2*log(sqrt(var2*2*M_PI)*p));
+        }
+        call->read_pos_bias = z;
+        //fprintf(stderr,"nref=%d  nalt=%d  U=%ld  p=%e var2=%e  zval=%e\n", nref,nalt,U, p,var2,call->read_pos_bias);
+    }
+}
+
+float mean_diff_to_prob(float mdiff, int dp, int readlen)
+{
+    if ( dp==2 )
+    {
+        if ( mdiff==0 )
+            return (2.0*readlen + 4.0*(readlen-1.0))/((float)readlen*readlen);
+        else
+            return 8.0*(readlen - 4.0*mdiff)/((float)readlen*readlen);
+    }
+
+    // This is crude empirical approximation and is not very accurate for
+    // shorter read lengths (<100bp). There certainly is a room for
+    // improvement.
+    const float mv[24][2] = { {0,0}, {0,0}, {0,0},
+        { 9.108, 4.934}, { 9.999, 3.991}, {10.273, 3.485}, {10.579, 3.160},
+        {10.828, 2.889}, {11.014, 2.703}, {11.028, 2.546}, {11.244, 2.391},
+        {11.231, 2.320}, {11.323, 2.138}, {11.403, 2.123}, {11.394, 1.994},
+        {11.451, 1.928}, {11.445, 1.862}, {11.516, 1.815}, {11.560, 1.761},
+        {11.544, 1.728}, {11.605, 1.674}, {11.592, 1.652}, {11.674, 1.613},
+        {11.641, 1.570} };
+
+    float m, v;
+    if ( dp>=24 )
+    {
+        m = readlen/8.;
+        if (dp>100) dp = 100;
+        v = 1.476/(0.182*pow(dp,0.514));
+        v = v*(readlen/100.);
+    }
+    else
+    {
+        m = mv[dp][0];
+        v = mv[dp][1];
+        m = m*readlen/100.;
+        v = v*readlen/100.;
+        v *= 1.2;   // allow more variability
+    }
+    return 1.0/(v*sqrt(2*M_PI)) * exp(-0.5*((mdiff-m)/v)*((mdiff-m)/v));
+}
+
+void calc_vdb(bcf_callaux_t *bca, bcf_call_t *call)
+{
+    int i, dp = 0;
+    float mean_pos = 0, mean_diff = 0;
+    for (i=0; i<bca->npos; i++)
+    {
+        if ( !bca->alt_pos[i] ) continue;
+        dp += bca->alt_pos[i];
+        int j = i<bca->npos/2 ? i : bca->npos - i;
+        mean_pos += bca->alt_pos[i]*j;
+    }
+    if ( dp<2 )
+    {
+        call->vdb = -1;
+        return;
+    }
+    mean_pos /= dp;
+    for (i=0; i<bca->npos; i++)
+    {
+        if ( !bca->alt_pos[i] ) continue;
+        int j = i<bca->npos/2 ? i : bca->npos - i;
+        mean_diff += bca->alt_pos[i] * fabs(j - mean_pos);
+    }
+    mean_diff /= dp;
+    call->vdb = mean_diff_to_prob(mean_diff, dp, bca->npos);
+}
+
+/**
+ *  bcf_call_combine() - sets the PL array and VDB, RPB annotations, finds the top two alleles
+ *  @n:         number of samples
+ *  @calls:     each sample's calls
+ *  @bca:       auxiliary data structure for holding temporary values
+ *  @ref_base:  the reference base
+ *  @call:      filled with the annotations
+ */
+int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call)
 {
 	int ref4, i, j, qsum[4];
 	int64_t tmp;
@@ -103,6 +296,8 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
 	for (i = 0; i < n; ++i)
 		for (j = 0; j < 4; ++j)
 			qsum[j] += calls[i].qsum[j];
+    int qsum_tot=0;
+    for (j=0; j<4; j++) { qsum_tot += qsum[j]; call->qsum[j] = 0; }
 	for (j = 0; j < 4; ++j) qsum[j] = qsum[j] << 2 | j;
 	// find the top 2 alleles
 	for (i = 1; i < 4; ++i) // insertion sort
@@ -114,15 +309,24 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
 	call->a[0] = ref4;
 	for (i = 3, j = 1; i >= 0; --i) {
 		if ((qsum[i]&3) != ref4) {
-			if (qsum[i]>>2 != 0) call->a[j++] = qsum[i]&3;
+			if (qsum[i]>>2 != 0) 
+            {
+                if ( j<4 ) call->qsum[j] = (float)(qsum[i]>>2)/qsum_tot; // ref N can make j>=4
+                call->a[j++]  = qsum[i]&3;
+            }
 			else break;
 		}
+        else 
+            call->qsum[0] = (float)(qsum[i]>>2)/qsum_tot;
 	}
 	if (ref_base >= 0) { // for SNPs, find the "unseen" base
 		if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
 			call->unseen = j, call->a[j++] = qsum[i]&3;
 		call->n_alleles = j;
-	} else call->n_alleles = j;
+	} else {
+		call->n_alleles = j;
+		if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything
+	}
 	// set the PL array
 	if (call->n < n) {
 		call->n = n;
@@ -134,8 +338,8 @@ 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;
@@ -155,26 +359,52 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
 	}
 	// combine annotations
 	memset(call->anno, 0, 16 * sizeof(int));
-	for (i = call->depth = 0, tmp = 0; i < n; ++i) {
+	for (i = call->depth = call->ori_depth = 0, tmp = 0; i < n; ++i) {
 		call->depth += calls[i].depth;
+		call->ori_depth += calls[i].ori_depth;
 		for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j];
 	}
+
+    calc_vdb(bca, call);
+    calc_ReadPosBias(bca, call);
+
 	return 0;
 }
 
-int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP)
+int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag,
+				 const bcf_callaux_t *bca, const char *ref)
 {
 	extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
 	kstring_t s;
-	int i;
+	int i, j;
 	b->n_smpl = bc->n;
 	b->tid = tid; b->pos = pos; b->qual = 0;
 	s.s = b->str; s.m = b->m_str; s.l = 0;
 	kputc('\0', &s);
-	if (bc->ori_ref < 0) {
-		kputc('N', &s); kputc('\0', &s);
-		kputs("<INDEL>", &s); kputc('\0', &s);
-	} else {
+	if (bc->ori_ref < 0) { // an indel
+		// write REF
+		kputc(ref[pos], &s);
+		for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s);
+		kputc('\0', &s);
+		// write ALT
+		kputc(ref[pos], &s);
+		for (i = 1; i < 4; ++i) {
+			if (bc->a[i] < 0) break;
+			if (i > 1) {
+				kputc(',', &s); kputc(ref[pos], &s);
+			}
+			if (bca->indel_types[bc->a[i]] < 0) { // deletion
+				for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j)
+					kputc(ref[pos+1+j], &s);
+			} else { // insertion; cannot be a reference unless a bug
+				char *inscns = &bca->inscns[bc->a[i] * bca->maxins];
+				for (j = 0; j < bca->indel_types[bc->a[i]]; ++j)
+					kputc("ACGTN"[(int)inscns[j]], &s);
+				for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s);
+			}
+		}
+		kputc('\0', &s);
+	} else { // a SNP
 		kputc("ACGTN"[bc->ori_ref], &s); kputc('\0', &s);
 		for (i = 1; i < 5; ++i) {
 			if (bc->a[i] < 0) break;
@@ -185,29 +415,39 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc
 	}
 	kputc('\0', &s);
 	// INFO
-	kputs("I16=", &s);
+	if (bc->ori_ref < 0) ksprintf(&s,"INDEL;IS=%d,%f;", bca->max_support, bca->max_frac);
+	kputs("DP=", &s); kputw(bc->ori_depth, &s); kputs(";I16=", &s);
 	for (i = 0; i < 16; ++i) {
 		if (i) kputc(',', &s);
 		kputw(bc->anno[i], &s);
 	}
+    //ksprintf(&s,";RPS=%d,%f,%f", bc->read_pos.dp,bc->read_pos.avg,bc->read_pos.var);
+    ksprintf(&s,";QS=%f,%f,%f,%f", bc->qsum[0],bc->qsum[1],bc->qsum[2],bc->qsum[3]);
+    if (bc->vdb != -1)
+        ksprintf(&s, ";VDB=%e", bc->vdb);
+    if (bc->read_pos_bias != -1 )
+        ksprintf(&s, ";RPB=%e", bc->read_pos_bias);
 	kputc('\0', &s);
 	// FMT
 	kputs("PL", &s);
-	if (bcr) {
-		kputs(":DP", &s);
-		if (is_SP) kputs(":SP", &s);
+	if (bcr && fmt_flag) {
+		if (fmt_flag & B2B_FMT_DP) kputs(":DP", &s);
+		if (fmt_flag & B2B_FMT_DV) kputs(":DV", &s);
+		if (fmt_flag & B2B_FMT_SP) kputs(":SP", &s);
 	}
 	kputc('\0', &s);
 	b->m_str = s.m; b->str = s.s; b->l_str = s.l;
 	bcf_sync(b);
 	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;
+	if (bcr && fmt_flag) {
+		uint16_t *dp = (fmt_flag & B2B_FMT_DP)? b->gi[1].data : 0;
+		uint16_t *dv = (fmt_flag & B2B_FMT_DV)? b->gi[1 + ((fmt_flag & B2B_FMT_DP) != 0)].data : 0;
+		int32_t  *sp = (fmt_flag & B2B_FMT_SP)? b->gi[1 + ((fmt_flag & B2B_FMT_DP) != 0) + ((fmt_flag & B2B_FMT_DV) != 0)].data : 0;
 		for (i = 0; i < bc->n; ++i) {
 			bcf_callret1_t *p = bcr + i;
-			dp[i] = p->depth < 0xffff? p->depth : 0xffff;
-			if (is_SP) {
+			if (dp) dp[i] = p->depth  < 0xffff? p->depth  : 0xffff;
+			if (dv) dv[i] = p->n_supp < 0xffff? p->n_supp : 0xffff;
+			if (sp) {
 				if (p->anno[0] + p->anno[1] < 2 || p->anno[2] + p->anno[3] < 2
 					|| p->anno[0] + p->anno[2] < 2 || p->anno[1] + p->anno[3] < 2)
 				{