X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=54b8f91722b2f16ade955231e075764b3161d2d5;hb=599bea10bc3487a0cbdf505e792a21a13fee2b11;hp=32d050d68413aa18e6ba4ea688615579a539bf2b;hpb=df7cadac556f302bdd0bc48c235c2b61b699dfe1;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 32d050d..54b8f91 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -726,31 +726,20 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 			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_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0, (conf->flag&MPLP_FMT_SP));
+			bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0,
+						 (conf->flag&MPLP_FMT_SP), 0, 0);
 			bcf_write(bp, bh, b);
 			bcf_destroy(b);
-			// test if there is an indel
-			if (conf->flag&MPLP_REALN) {
-				for (i = 0; i < gplp.n; ++i) {
-					int j;
-					for (j = 0; j < gplp.n_plp[i]; ++j) {
-						const bam_pileup1_t *p = gplp.plp[i] + j;
-						if (p->indel != 0) break;
-					}
-					if (j != gplp.n_plp[i]) break;
-				}
-				if (i < gplp.n) { // at least one of the read contains a gap
-					for (i = 0; i < gplp.n; ++i)
-						bcf_call_glfgen_gap(pos, gplp.n_plp[i], gplp.plp[i], bca, bcr + i);
-					bcf_call_combine_gap(gplp.n, bcr, &bc);
-					if (bc.depth > 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));
-						bcf_write(bp, bh, b);
-						bcf_destroy(b);
-					}
-				}
+			// call indels
+			if (bcf_call_gap_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], -1, bca, bcr + i);
+				bcf_call_combine(gplp.n, bcr, -1, &bc);
+				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 {
 			printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');