* samtools-0.1.8-11 (r672)

[samtools.git] / bam2bcf.c

diff --git a/bam2bcf.c b/bam2bcf.c
index d69c771da80ef14ed925e549548f988a766ae680..5ad81c05641935ffd4c7f2b6082acc9d341214b2 100644 (file)
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -5,6 +5,8 @@
 #include "bam2bcf.h"
 #include "bcftools/bcf.h"
 
+#define MAX_END_DIST 30
+
 extern void ks_introsort_uint32_t(size_t n, uint32_t a[]);
 
 #define CALL_ETA 0.03f
@@ -12,18 +14,19 @@ extern      void ks_introsort_uint32_t(size_t n, uint32_t a[]);
 #define CALL_DEFTHETA 0.85f
 
 struct __bcf_callaux_t {
-       int max_info, capQ;
+       int max_info, capQ, min_baseQ;
        double *fk;
        uint32_t *info;
 };
 
-bcf_callaux_t *bcf_call_init(double theta)
+bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
 {
        bcf_callaux_t *bca;
        int n;
        if (theta <= 0.) theta = CALL_DEFTHETA;
        bca = calloc(1, sizeof(bcf_callaux_t));
        bca->capQ = 60;
+       bca->min_baseQ = min_baseQ;
        bca->fk = calloc(CALL_MAX, sizeof(double));
        bca->fk[0] = 1.;
        for (n = 1; n < CALL_MAX; ++n)
@@ -70,11 +73,12 @@ typedef struct {
  */
 int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf_callaux_t *bca, bcf_callret1_t *r)
 {
-       int i, j, k, c, n;
+       int i, j, k, c, n, ref4;
        float *p = r->p;
        auxaux_t aux;
 
        memset(r, 0, sizeof(bcf_callret1_t));
+       ref4 = bam_nt16_nt4_table[ref_base];
        if (_n == 0) return -1;
 
        // enlarge the aux array if necessary
@@ -87,16 +91,27 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf
        for (i = n = 0; i < _n; ++i) {
                const bam_pileup1_t *p = pl + i;
                uint32_t q, x = 0, qq;
+               int min_dist;
                if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue; // skip unmapped reads and deleted bases
                q = (uint32_t)bam1_qual(p->b)[p->qpos]; // base quality
+               if (q < bca->min_baseQ) continue;
                x |= (uint32_t)bam1_strand(p->b) << 18 | q << 8 | p->b->core.qual;
                if (p->b->core.qual < q) q = p->b->core.qual; // cap the overall quality at mapping quality
                x |= q << 24;
                qq = bam1_seqi(bam1_seq(p->b), p->qpos); // base
                q = bam_nt16_nt4_table[qq? qq : ref_base]; // q is the 2-bit base
                if (q < 4) x |= 1 << 21 | q << 16;
-               
+               k = (ref4 < 4 && q == ref4)? 0 : 1;
+               k = k<<1 | bam1_strand(p->b);
+               ++r->d[k];
                bca->info[n++] = x;
+               // calculate min_dist
+               min_dist = p->b->core.l_qseq - 1 - p->qpos;
+               if (min_dist > p->qpos) min_dist = p->qpos;
+               if (min_dist > MAX_END_DIST) min_dist = MAX_END_DIST;
+               k >>= 1;
+               r->dsum[k]  += min_dist;
+               r->d2sum[k] += min_dist * min_dist;
        }
        ks_introsort_uint32_t(n, bca->info);
        r->depth = n;
@@ -137,17 +152,9 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf
                        p[j*5+k] = p[k*5+j] = 3.01 * (aux.c[j] + aux.c[k]) + tmp;
                }
        }
-       return 0;
+       return r->depth;
 }
 
-/*
-  1) Find the top 2 bases (from esum[4]).
-
-  2) If the reference base is among the top 2, consider the locus is
-     potentially biallelic and set call->a[2] as -1; otherwise, the
-     locus is potentially triallelic. If the reference is ambiguous,
-     take the weakest call as the pseudo-reference.
- */
 int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call)
 {
        int ref4, i, j;
@@ -210,10 +217,26 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
                }
                call->shift = (int)(sum_min + .499);
        }
+       memset(call->d, 0, 4 * sizeof(int));
+       call->davg[0] = call->davg[1] = call->dstd[0] = call->dstd[1] = 0.;
        for (i = call->depth = 0, tmp = 0; i < n; ++i) {
                call->depth += calls[i].depth;
+               for (j = 0; j < 4; ++j) call->d[j] += calls[i].d[j];
+               for (j = 0; j < 2; ++j) {
+                       call->davg[j] += calls[i].dsum[j];
+                       call->dstd[j] += calls[i].d2sum[j];
+               }
                tmp += calls[i].sum_Q2;
        }
+       for (j = 0; j < 2; ++j) {
+               int x = call->d[j*2] + call->d[j*2+1];
+               if (x == 0) {
+                       call->davg[j] = call->dstd[j] = 0.;
+               } else {
+                       call->davg[j] /= x;
+                       call->dstd[j] = sqrt(call->dstd[j] / x - call->davg[j] * call->davg[j]);
+               }
+       }
        call->rmsQ = (int)(sqrt((double)tmp / call->depth) + .499);
        return 0;
 }
@@ -234,7 +257,17 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b)
        }
        kputc('\0', &s);
        kputc('\0', &s);
-       kputs("MQ=", &s); kputw(bc->rmsQ, &s); kputs(";DP=", &s); kputw(bc->depth, &s); kputc('\0', &s);
+       // INFO
+       kputs("MQ=", &s); kputw(bc->rmsQ, &s); // kputs(";DP=", &s); kputw(bc->depth, &s);
+       kputs(";DP4=", &s);
+       for (i = 0; i < 4; ++i) {
+               if (i) kputc(',', &s);
+               kputw(bc->d[i], &s);
+       }
+       if (bc->d[2] + bc->d[3] > 1)
+               ksprintf(&s, ";MED=%.1lf,%.1lf,%.1lf,%.1lf", bc->davg[0], bc->dstd[0], bc->davg[1], bc->dstd[1]);
+       kputc('\0', &s);
+       // FMT
        kputs("PL", &s); kputc('\0', &s);
        b->m_str = s.m; b->str = s.s; b->l_str = s.l;
        bcf_sync(bc->n, b);