X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=002297a1229678a256e9045f420b89d5f273b1ea;hb=82797ab5f5ba03634967e19822e11a491c8e6198;hp=7f13eee4ed51a987a6386796eb4eeae2bad65891;hpb=4c8c9dfc1e3b3b066a62a703fd3ba04db6ad5a45;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 7f13eee..002297a 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -563,9 +563,10 @@ static int mplp_func(void *data, bam1_t *b)
 	mplp_aux_t *ma = (mplp_aux_t*)data;
 	int ret, skip = 0;
 	do {
-		int has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
+		int has_ref;
 		ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
 		if (ret < 0) break;
+		has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
 		skip = 0;
 		if (has_ref && (ma->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, 1);
 		if (has_ref && ma->capQ_thres > 10) {
@@ -738,31 +739,16 @@ 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 {