* this revision is UNSTABLE

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index ed230e8fb8c763388f57a272acee2ca5f96e7503..32d050d68413aa18e6ba4ea688615579a539bf2b 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -742,6 +742,14 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                                if (i < gplp.n) { // at least one of the read contains a gap
                                        for (i = 0; i < gplp.n; ++i)
                                                bcf_call_glfgen_gap(pos, gplp.n_plp[i], gplp.plp[i], bca, bcr + i);
+                                       bcf_call_combine_gap(gplp.n, bcr, &bc);
+                                       if (bc.depth > 0) {
+                                               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));
+                                               bcf_write(bp, bh, b);
+                                               bcf_destroy(b);
+                                       }
                                }
                        }
                } else {