* samtools-0.1.9-2 (r797)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index b56f879dfbf226e70bc07c7b2853705c6584f92f..54b8f91722b2f16ade955231e075764b3161d2d5 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -726,7 +726,8 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        for (i = 0; i < gplp.n; ++i)
                                bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
                        bcf_call_combine(gplp.n, bcr, ref16, &bc);
-                       bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0, (conf->flag&MPLP_FMT_SP));
+                       bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0,
+                                                (conf->flag&MPLP_FMT_SP), 0, 0);
                        bcf_write(bp, bh, b);
                        bcf_destroy(b);
                        // call indels
@@ -736,7 +737,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                                bcf_call_combine(gplp.n, bcr, -1, &bc);
                                b = calloc(1, sizeof(bcf1_t));
                                bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0,
-                                                        (conf->flag&MPLP_FMT_SP));
+                                                        (conf->flag&MPLP_FMT_SP), bca, ref);
                                bcf_write(bp, bh, b);
                                bcf_destroy(b);
                        }