X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=blobdiff_plain;f=bam2bcf.c;h=a51a406f249c05834b0d8e20f49403d5ed29a3b6;hp=dec3305340f689a100d29dc4f9b5998e7692c6d4;hb=307c147168f7154e3755712797078c513e0b242a;hpb=cb5f44947629a68d16a48d32eef6e42a66e482fe

diff --git a/bam2bcf.c b/bam2bcf.c
index dec3305..a51a406 100644
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -26,6 +26,7 @@ bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
 	bca->e = errmod_init(1. - theta);
 	bca->min_frac = 0.002;
 	bca->min_support = 1;
+    bca->per_sample_flt = 0;
 	return bca;
 }
 
@@ -54,8 +55,7 @@ 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, seqQ;
 		// set base
@@ -78,6 +78,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
 			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
 		if (b < 4) r->qsum[b] += q;
@@ -86,9 +87,9 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
 		if (min_dist > p->qpos) min_dist = p->qpos;
 		if (min_dist > CAP_DIST) min_dist = CAP_DIST;
 		r->anno[1<<2|is_diff<<1|0] += baseQ;
-		r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ;
+		r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ;	// FIXME: signed int is not enough for thousands of samples
 		r->anno[2<<2|is_diff<<1|0] += mapQ;
-		r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
+		r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;		// FIXME: signed int is not enough for thousands of samples
 		r->anno[3<<2|is_diff<<1|0] += min_dist;
 		r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
 	}
@@ -194,6 +195,8 @@ 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
@@ -205,9 +208,15 @@ 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)
@@ -260,7 +269,7 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
 	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);
@@ -304,34 +313,36 @@ 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);
+	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);
 	}
-    if ( bc->vdb!=1 )
-    {
+    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=%.4f", bc->vdb);
-    }
 	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;
-		int32_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)
 				{