X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.c;h=f263fad55a5d1f1438fd50d127fb2362309f100b;hb=3384f6c6c1642ada4edae9204ca1202672de7d5a;hp=46f534ee7553182f790384921c8c667417838b75;hpb=c1e9248358a76e932de6f21039e56dbca9950dae;p=samtools.git

diff --git a/bam2bcf.c b/bam2bcf.c
index 46f534e..f263fad 100644
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -79,7 +79,7 @@ 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;
@@ -144,8 +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;
@@ -236,7 +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;