* samtools-0.1.9-16 (r822)

[samtools.git] / bam2bcf.c

diff --git a/bam2bcf.c b/bam2bcf.c
index 8537e232191189ee489ba7ce681008c12a39b829..088635c0b04a549b762d1a3b28efad82f4bb5c80 100644 (file)
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -36,7 +36,7 @@ void bcf_call_destroy(bcf_callaux_t *bca)
  * negative if we are looking at an indel. */
 int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r)
 {
-       int i, n, ref4, is_indel;
+       int i, n, ref4, is_indel, ori_depth = 0;
        memset(r, 0, sizeof(bcf_callret1_t));
        if (ref_base >= 0) {
                ref4 = bam_nt16_nt4_table[ref_base];
@@ -56,6 +56,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
                int q, b, mapQ, baseQ, is_diff, min_dist, seqQ;
                // set base
                if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue;
+               ++ori_depth;
                baseQ = q = is_indel? p->aux&0xff : (int)bam1_qual(p->b)[p->qpos]; // base/indel quality
                seqQ = is_indel? (p->aux>>8&0xff) : 99;
                if (q < bca->min_baseQ) continue;
@@ -86,7 +87,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
                r->anno[3<<2|is_diff<<1|0] += min_dist;
                r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
        }
-       r->depth = n;
+       r->depth = n; r->ori_depth = ori_depth;
        // glfgen
        errmod_cal(bca->e, n, 5, bca->bases, r->p);
        return r->depth;
@@ -160,8 +161,9 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
        }
        // combine annotations
        memset(call->anno, 0, 16 * sizeof(int));
-       for (i = call->depth = 0, tmp = 0; i < n; ++i) {
+       for (i = call->depth = call->ori_depth = 0, tmp = 0; i < n; ++i) {
                call->depth += calls[i].depth;
+               call->ori_depth += calls[i].ori_depth;
                for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j];
        }
        return 0;
@@ -212,7 +214,7 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc
        kputc('\0', &s);
        // INFO
        if (bc->ori_ref < 0) kputs("INDEL;", &s);
-       kputs("I16=", &s);
+       kputs("DP=", &s); kputw(bc->ori_depth, &s); kputs(";I16=", &s);
        for (i = 0; i < 16; ++i) {
                if (i) kputc(',', &s);
                kputw(bc->anno[i], &s);