for backup. no effective changes

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index a3e6aeb614927733676b2b25e4592786cb14ef2e..ed230e8fb8c763388f57a272acee2ca5f96e7503 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -729,6 +729,21 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        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);
+                       // 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);
+                               }
+                       }
                } else {
                        printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
                        for (i = 0; i < n; ++i) {