backup commit

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 51dece53796f23563c2943e77c8482f70ddef1d5..3f5d424826ddee9952b6c4f2fcf17e3c2c40688f 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -312,7 +312,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        ref16 = bam_nt16_table[_ref0];
                        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_call_combine(gplp.n, bcr, bca, ref16, &bc);
                        bcf_call2bcf(tid, pos, &bc, b, bcr, conf->fmt_flag, 0, 0);
                        bcf_write(bp, bh, b);
                        bcf_destroy(b);
@@ -320,7 +320,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) {
                                for (i = 0; i < gplp.n; ++i)
                                        bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i);
-                               if (bcf_call_combine(gplp.n, bcr, -1, &bc) >= 0) {
+                               if (bcf_call_combine(gplp.n, bcr, bca, -1, &bc) >= 0) {
                                        b = calloc(1, sizeof(bcf1_t));
                                        bcf_call2bcf(tid, pos, &bc, b, bcr, conf->fmt_flag, bca, ref);
                                        bcf_write(bp, bh, b);