From: Heng Li <lh3@live.co.uk>
Date: Fri, 23 Jul 2010 17:25:44 +0000 (+0000)
Subject: added an alternative prior
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=71355852e510ac7937d552117557b9dbf07cd557

added an alternative prior
---

diff --git a/bam_mcns.c b/bam_mcns.c
index c1cdb90..7859169 100644
--- a/bam_mcns.c
+++ b/bam_mcns.c
@@ -9,20 +9,23 @@
 struct __mc_aux_t {
 	int n, N;
 	int ref, alt;
-	double theta;
 	double *q2p, *pdg; // pdg -> P(D|g)
 	double *alpha, *beta;
 	int *qsum, *bcnt;
 };
 
-void mc_init_prior(mc_aux_t *ma, double theta)
+void mc_init_prior(mc_aux_t *ma, int type, double theta)
 {
-	double sum;
 	int i;
-	ma->theta = theta;
-	for (i = 0, sum = 0.; i < 2 * ma->n; ++i)
-		sum += (ma->alpha[i] = ma->theta / (2 * ma->n - i));
-	ma->alpha[2 * ma->n] = 1. - sum;
+	if (type == MC_PTYPE_COND2) {
+		for (i = 0; i <= 2 * ma->n; ++i)
+			ma->alpha[i] = 2. * (i + 1) / (2 * ma->n + 1) / (2 * ma->n + 2);
+	} else {
+		double sum;
+		for (i = 0, sum = 0.; i < 2 * ma->n; ++i)
+			sum += (ma->alpha[i] = theta / (2 * ma->n - i));
+		ma->alpha[2 * ma->n] = 1. - sum;
+	}
 }
 
 mc_aux_t *mc_init(int n) // FIXME: assuming diploid
@@ -46,7 +49,7 @@ mc_aux_t *mc_init(int n) // FIXME: assuming diploid
 		bi[1] = 2 * f * (1. - f);
 		bi[2] = f * f;
 	}
-	mc_init_prior(ma, 1e-3); // the simplest prior
+	mc_init_prior(ma, MC_PTYPE_FULL, 1e-3); // the simplest prior
 	return ma;
 }
 
diff --git a/bam_mcns.h b/bam_mcns.h
index 89879fb..cff6e57 100644
--- a/bam_mcns.h
+++ b/bam_mcns.h
@@ -6,11 +6,15 @@
 struct __mc_aux_t;
 typedef struct __mc_aux_t mc_aux_t;
 
+#define MC_PTYPE_FULL  1
+#define MC_PTYPE_COND2 2
+
 #ifdef __cplusplus
 extern "C" {
 #endif
 
 	mc_aux_t *mc_init(int n);
+	void mc_init_prior(mc_aux_t *ma, int type, double theta);
 	void mc_destroy(mc_aux_t *ma);
 	double mc_freq0(int ref, int *n, const bam_pileup1_t **plp, mc_aux_t *ma, int *_ref, int *alt);
 	double mc_freq_iter(double f0, mc_aux_t *ma);
diff --git a/bam_plcmd.c b/bam_plcmd.c
index 258b83f..82fcafc 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -450,7 +450,8 @@ int bam_pileup(int argc, char *argv[])
  ***********/
 
 typedef struct {
-	int vcf, max_mq, min_mq, var_only;
+	int vcf, max_mq, min_mq, var_only, prior_type;
+	double theta;
 	char *reg, *fn_pos;
 	faidx_t *fai;
 	kh_64_t *hash;
@@ -537,7 +538,10 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 		free(s.s);
 	}
 	// mpileup
-	if (conf->vcf) ma = mc_init(n);
+	if (conf->vcf) {
+		ma = mc_init(n);
+		mc_init_prior(ma, conf->prior_type, conf->theta);
+	}
 	ref_tid = -1; ref = 0;
 	iter = bam_mplp_init(n, mplp_func, (void**)data);
 	while (bam_mplp_auto(iter, &tid, &pos, n_plp, plp) > 0) {
@@ -650,8 +654,12 @@ int bam_mpileup(int argc, char *argv[])
 	mplp_conf_t mplp;
 	memset(&mplp, 0, sizeof(mplp_conf_t));
 	mplp.max_mq = 60;
-	while ((c = getopt(argc, argv, "f:r:l:VvM:q:")) >= 0) {
+	mplp.prior_type = MC_PTYPE_FULL;
+	mplp.theta = 1e-3;
+	while ((c = getopt(argc, argv, "f:r:l:VvM:q:t:2")) >= 0) {
 		switch (c) {
+		case 't': mplp.theta = atof(optarg); break;
+		case '2': mplp.prior_type = MC_PTYPE_COND2; break;
 		case 'f':
 			mplp.fai = fai_load(optarg);
 			if (mplp.fai == 0) return 1;
@@ -672,8 +680,10 @@ int bam_mpileup(int argc, char *argv[])
 		fprintf(stderr, "         -l FILE     list of positions (format: chr pos) [null]\n");
 		fprintf(stderr, "         -M INT      cap mapping quality at INT [%d]\n", mplp.max_mq);
 		fprintf(stderr, "         -q INT      filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
+		fprintf(stderr, "         -t FLOAT    scaled mutation rate [%lg]\n", mplp.theta);
 		fprintf(stderr, "         -V          generate VCF output (SNP calling)\n");
 		fprintf(stderr, "         -v          show variant sites only\n");
+		fprintf(stderr, "         -2          conditional prior\n");
 		fprintf(stderr, "\n");
 		fprintf(stderr, "Notes: Assuming error independency and diploid individuals.\n\n");
 		return 1;
diff --git a/bamtk.c b/bamtk.c
index b51df96..1de3920 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.8-3 (r627)"
+#define PACKAGE_VERSION "0.1.8-4 (r631)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);