added an alternative prior

diff --git a/bam_mcns.c b/bam_mcns.c
index c1cdb9077ff7b9278f631c5da3915348114ae5c9..7859169c9ef8799b37878a6d1e19e7c1c5b8fcb0 100644 (file)
--- 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 89879fbc0f9cb76e924b8911fdc74442bc513c88..cff6e57d28047950be347e7d873d940638baa385 100644 (file)
--- 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 258b83fd72b6ac21db863ea837d46c92d0ff0aef..82fcafc7f9c8836d839aef7ecaf26291ed1f89a0 100644 (file)
--- 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 b51df96501415599e114cec3ac06353ff539de1b..1de39203b25a4ee526588358c7ce19cd6916b650 100644 (file)
--- 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[]);