prepare for the indel caller. It is not ready yet.

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index a3e6aeb614927733676b2b25e4592786cb14ef2e..1b15aaec8b274e5ba92af6470c71a2f913f2a480 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -729,6 +729,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        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);
+//                     bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref);
                } else {
                        printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
                        for (i = 0; i < n; ++i) {