changes from git

[samtools.git] / bam2bcf.c

diff --git a/bam2bcf.c b/bam2bcf.c
index dec3305340f689a100d29dc4f9b5998e7692c6d4..83f2e564b67b85c711b0a0b83d1e29fc52591eb5 100644 (file)
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -55,7 +55,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
        }
        // fill the bases array
        memset(r, 0, sizeof(bcf_callret1_t));
-       for (i = n = 0; i < _n; ++i) {
+       for (i = n = r->n_supp = 0; i < _n; ++i) {
                const bam_pileup1_t *p = pl + i;
                int q, b, mapQ, baseQ, is_diff, min_dist, seqQ;
                // set base
@@ -78,6 +78,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
                        b = p->aux>>16&0x3f;
                        is_diff = (b != 0);
                }
+               if (is_diff) ++r->n_supp;
                bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
                // collect annotations
                if (b < 4) r->qsum[b] += q;
@@ -260,7 +261,7 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
        return 0;
 }
 
-int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
+int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag,
                                 const bcf_callaux_t *bca, const char *ref)
 {
        extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
@@ -310,28 +311,29 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc
                if (i) kputc(',', &s);
                kputw(bc->anno[i], &s);
        }
-    if ( bc->vdb!=1 )
-    {
+    if (bc->vdb != 1)
         ksprintf(&s, ";VDB=%.4f", bc->vdb);
-    }
        kputc('\0', &s);
        // FMT
        kputs("PL", &s);
-       if (bcr) {
-               kputs(":DP", &s);
-               if (is_SP) kputs(":SP", &s);
+       if (bcr && fmt_flag) {
+               if (fmt_flag & B2B_FMT_DP) kputs(":DP", &s);
+               if (fmt_flag & B2B_FMT_DV) kputs(":DV", &s);
+               if (fmt_flag & B2B_FMT_SP) kputs(":SP", &s);
        }
        kputc('\0', &s);
        b->m_str = s.m; b->str = s.s; b->l_str = s.l;
        bcf_sync(b);
        memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n);
-       if (bcr) {
-               uint16_t *dp = (uint16_t*)b->gi[1].data;
-               int32_t *sp = is_SP? b->gi[2].data : 0;
+       if (bcr && fmt_flag) {
+               uint16_t *dp = (fmt_flag & B2B_FMT_DP)? b->gi[1].data : 0;
+               uint16_t *dv = (fmt_flag & B2B_FMT_DV)? b->gi[1 + ((fmt_flag & B2B_FMT_DP) != 0)].data : 0;
+               int32_t  *sp = (fmt_flag & B2B_FMT_DV)? b->gi[1 + ((fmt_flag & B2B_FMT_DP) != 0) + ((fmt_flag & B2B_FMT_DV) != 0)].data : 0;
                for (i = 0; i < bc->n; ++i) {
                        bcf_callret1_t *p = bcr + i;
-                       dp[i] = p->depth < 0xffff? p->depth : 0xffff;
-                       if (is_SP) {
+                       if (dp) dp[i] = p->depth  < 0xffff? p->depth  : 0xffff;
+                       if (dv) dv[i] = p->n_supp < 0xffff? p->n_supp : 0xffff;
+                       if (sp) {
                                if (p->anno[0] + p->anno[1] < 2 || p->anno[2] + p->anno[3] < 2
                                        || p->anno[0] + p->anno[2] < 2 || p->anno[1] + p->anno[3] < 2)
                                {