* samtools-0.1.8-18 (r763)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index af43918f1ba0ea1d80ef86ecfbe75ac9e3553ad4..c8ab7ba8dc2535940ca6b30fe43d0d2206207594 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -461,7 +461,6 @@ int bam_pileup(int argc, char *argv[])
 
 typedef struct {
        int max_mq, min_mq, flag, min_baseQ, capQ_thres;
-       double theta;
        char *reg, *fn_pos;
        faidx_t *fai;
        kh_64_t *hash;
@@ -698,12 +697,10 @@ int bam_mpileup(int argc, char *argv[])
        mplp_conf_t mplp;
        memset(&mplp, 0, sizeof(mplp_conf_t));
        mplp.max_mq = 60;
-       mplp.theta = 1e-3;
        mplp.min_baseQ = 13;
        mplp.capQ_thres = 0;
-       while ((c = getopt(argc, argv, "gf:r:l:M:q:t:Q:uaORC:")) >= 0) {
+       while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:")) >= 0) {
                switch (c) {
-               case 't': mplp.theta = atof(optarg); break;
                case 'f':
                        mplp.fai = fai_load(optarg);
                        if (mplp.fai == 0) return 1;
@@ -711,7 +708,7 @@ int bam_mpileup(int argc, char *argv[])
                case 'r': mplp.reg = strdup(optarg); break;
                case 'l': mplp.fn_pos = strdup(optarg); break;
                case 'g': mplp.flag |= MPLP_GLF; break;
-               case 'u': mplp.flag |= MPLP_NO_COMP; break;
+               case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
                case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
                case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
                case 'R': mplp.flag |= MPLP_REALN; break;
@@ -730,7 +727,6 @@ int bam_mpileup(int argc, char *argv[])
                fprintf(stderr, "         -M INT      cap mapping quality at INT [%d]\n", mplp.max_mq);
                fprintf(stderr, "         -Q INT      min base quality [%d]\n", mplp.min_baseQ);
                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, "         -g          generate BCF output\n");
                fprintf(stderr, "         -u          do not compress BCF output\n");
                fprintf(stderr, "\n");