X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_mcns.c;h=dee2016507100888faf053163ec47a8b8b474828;hb=d763698cc12d7daa7361d610db3c9c9e83e7655b;hp=cd64b0ac139814706632a05d2e7b75d619a36b8a;hpb=d73a1b3b94255044787c0e4bfeba37df66e99770;p=samtools.git

diff --git a/bam_mcns.c b/bam_mcns.c
index cd64b0a..dee2016 100644
--- a/bam_mcns.c
+++ b/bam_mcns.c
@@ -12,7 +12,7 @@ struct __mc_aux_t {
 	double theta;
 	double *q2p, *pdg; // pdg -> P(D|g)
 	double *alpha, *beta;
-	int *qsum, *bcnt, rcnt[4];
+	int *qsum, *bcnt;
 };
 
 void mc_init_prior(mc_aux_t *ma, double theta)
@@ -65,11 +65,9 @@ static void sum_err(int *n, const bam_pileup1_t **plp, mc_aux_t *ma)
 	int i, j;
 	memset(ma->qsum, 0, sizeof(int) * 4 * ma->n);
 	memset(ma->bcnt, 0, sizeof(int) * 4 * ma->n);
-	memset(ma->rcnt, 0, sizeof(int) * 4);
 	for (j = 0; j < ma->n; ++j) {
 		int tmp, *qsum = ma->qsum + j * 4;
 		int *bcnt = ma->bcnt + j * 4;
-		double r = drand48(), rr;
 		for (i = tmp = 0; i < n[j]; ++i) {
 			const bam_pileup1_t *p = plp[j] + i;
 			int q, b;
@@ -83,13 +81,6 @@ static void sum_err(int *n, const bam_pileup1_t **plp, mc_aux_t *ma)
 			++bcnt[b];
 			++tmp;
 		}
-		if (tmp) {
-			for (i = 0, rr = 0.; i < 4; ++i) {
-				rr += (double)bcnt[i] / tmp;
-				if (rr >= r) break;
-			}
-			if (i < 4) ++ma->rcnt[i];
-		}
 	}
 }
 
@@ -127,21 +118,21 @@ static void cal_pdg(mc_aux_t *ma)
 // return the reference allele frequency
 double mc_freq0(int ref, int *n, const bam_pileup1_t **plp, mc_aux_t *ma, int *_ref, int *alt)
 {
-	int i, acnt[4], j;
-	double fr = -1., f0 = -1.;
+	int i, cnt;
+	double f;
 	sum_err(n, plp, ma);
 	set_allele(ref, ma);
 	cal_pdg(ma);
-	acnt[0] = acnt[1] = acnt[2] = acnt[3] = 0;
-	for (i = 0; i < ma->n; ++i)
-		for (j = 0; j < 4; ++j)
-			acnt[j] += ma->bcnt[i * 4 + j];
-	if (ma->rcnt[ma->ref] + ma->rcnt[ma->alt]) // never used...
-		fr = (double)ma->rcnt[ref] / (ma->rcnt[ma->ref] + ma->rcnt[ma->alt]);
-	if (acnt[ma->ref] + acnt[ma->alt])
-		f0 = (double)acnt[ref] / (acnt[ma->ref] + acnt[ma->alt]);
 	*_ref = ma->ref; *alt = ma->alt;
-	return ma->n == 1 || fr < 0.? f0 : fr;
+	for (i = cnt = 0, f = 0.; i < ma->n; ++i) {
+		int *bcnt = ma->bcnt + i * 4;
+		int x = bcnt[ma->ref] + bcnt[ma->alt];
+		if (x) {
+			++cnt;
+			f += (double)bcnt[ma->ref] / x;
+		}
+	}
+	return f / cnt;
 }
 // f0 is the reference allele frequency
 double mc_freq_iter(double f0, mc_aux_t *ma)