added an alternative prior

[samtools.git] / bam_plcmd.c

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;