* samtools-0.1.11-1 (r858)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 7f13eee4ed51a987a6386796eb4eeae2bad65891..002297a1229678a256e9045f420b89d5f273b1ea 100644 (file)
--- 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 {