X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=e3f73aaddd03a14343a82084ee060d9c41ba42d4;hb=30004e9139b96449fa34831af2fd8e860567a29d;hp=7f13eee4ed51a987a6386796eb4eeae2bad65891;hpb=ea1bf85308be7146d11a0153391d99fcfb3f83ad;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 7f13eee..e3f73aa 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -738,31 +738,16 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 						 (conf->flag&MPLP_FMT_SP), 0, 0);
 			bcf_write(bp, bh, b);
 			bcf_destroy(b);
-			if (!(conf->flag&MPLP_NO_INDEL)) {
-				// call MNPs
-				if (bcf_call_mnp_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref) >= 0) {
-					for (i = 0; i < gplp.n; ++i)
-						bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], B2B_REF_MNP, bca, bcr + i);
-					if (bcf_call_combine(gplp.n, bcr, B2B_REF_MNP, &bc) >= 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), bca, ref);
-						bcf_write(bp, bh, b);
-						bcf_destroy(b);
-						bca->last_mnp_pos = pos;
-					}
-				}
-				// call indels
-				if (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], B2B_REF_INDEL, bca, bcr + i);
-					if (bcf_call_combine(gplp.n, bcr, B2B_REF_INDEL, &bc) >= 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), bca, ref);
-						bcf_write(bp, bh, b);
-						bcf_destroy(b);
-					}
+			// call indels
+			if (!(conf->flag&MPLP_NO_INDEL) && 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) {
+					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), bca, ref);
+					bcf_write(bp, bh, b);
+					bcf_destroy(b);
 				}
 			}
 		} else {