X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=blobdiff_plain;f=bam_plcmd.c;h=9c4f273dcbfe2c3576e9c6ea0e2d7661839bbb85;hp=8935c5a2f52437057596f6e35ab74dc85a2a569c;hb=60e0a8467ddbd0b89f15d201dcfe10c8796552b2;hpb=607d7a0ab79152be4153fa09861cfa889488f2c7

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 8935c5a..9c4f273 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -220,6 +220,10 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
         }
 		data[i]->conf = conf;
 		h_tmp = bam_header_read(data[i]->fp);
+        if ( !h_tmp ) {
+            fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, fn[i]);
+            exit(1);
+        }
 		data[i]->h = i? h : h_tmp; // for i==0, "h" has not been set yet
 		bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text);
 		rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
@@ -317,7 +321,7 @@ 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);
@@ -325,7 +329,7 @@ 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);