X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.c;h=f263fad55a5d1f1438fd50d127fb2362309f100b;hb=d195bcfb6632c68032a89c091c20dc24dd6ded60;hp=384e481cbc5e6d9d4cae4f2e50a66008f29f1c84;hpb=e2d4caa430112346f387709bd016eb1a8c737d8e;p=samtools.git

diff --git a/bam2bcf.c b/bam2bcf.c
index 384e481..f263fad 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
 
@@ -20,9 +21,11 @@ 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;
 }
 
@@ -36,7 +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)
 {
-	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];
@@ -53,12 +56,16 @@ 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;
-		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 +74,12 @@ 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;
 		// 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;
@@ -84,7 +91,7 @@ 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 +129,10 @@ 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;
@@ -134,8 +144,8 @@ 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;
@@ -155,8 +165,9 @@ 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;
@@ -207,7 +218,7 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc
 	kputc('\0', &s);
 	// INFO
 	if (bc->ori_ref < 0) kputs("INDEL;", &s);
-	kputs("I16=", &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);
@@ -225,7 +236,7 @@ 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;