X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.c;h=08120fc46c2a3902e01582b45de0659d4b333eb6;hb=d062f8f3ca3f897b7a95c81e76d05e94b1d39877;hp=de6a3ed367b90bea3a4fc7430c9f4b4fa5bf26e4;hpb=917ed8ca3a137ff2c2db887c0c72f3cce09f7df4;p=samtools.git

diff --git a/bam2bcf.c b/bam2bcf.c
index de6a3ed..08120fc 100644
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -20,9 +20,11 @@ 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);
+	bca->min_frac = 0.002;
+	bca->min_support = 1;
 	return bca;
 }
 
@@ -30,13 +32,13 @@ void bcf_call_destroy(bcf_callaux_t *bca)
 {
 	if (bca == 0) return;
 	errmod_destroy(bca->e);
-	free(bca->bases); free(bca);
+	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];
@@ -53,11 +55,14 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
 	memset(r, 0, sizeof(bcf_callret1_t));
 	for (i = n = 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;
+		if (q > seqQ) q = seqQ;
 		mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ;
 		if (q > mapQ) q = mapQ;
 		if (q > 63) q = 63;
@@ -67,7 +72,7 @@ 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);
 		}
 		bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
@@ -84,7 +89,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
 		r->anno[3<<2|is_diff<<1|0] += min_dist;
 		r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
 	}
-	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;
@@ -122,7 +127,10 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
 		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;
@@ -155,26 +163,48 @@ 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];
 	}
 	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 is_SP,
+				 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;
@@ -185,7 +215,8 @@ 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) kputs("INDEL;", &s);
+	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);