* bcftools: add HWE (no testing for now)

[samtools.git] / bam2bcf.c

diff --git a/bam2bcf.c b/bam2bcf.c
index 5ad81c05641935ffd4c7f2b6082acc9d341214b2..1f7a0c042b2dad49abe5bb9d1668d90ddc96edf5 100644 (file)
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -5,7 +5,7 @@
 #include "bam2bcf.h"
 #include "bcftools/bcf.h"
 
-#define MAX_END_DIST 30
+#define END_DIST_THRES 11
 
 extern void ks_introsort_uint32_t(size_t n, uint32_t a[]);
 
@@ -108,10 +108,8 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf
                // 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;
+               k = (k&2) | (min_dist <= END_DIST_THRES);
+               ++r->ed[k];
        }
        ks_introsort_uint32_t(n, bca->info);
        r->depth = n;
@@ -218,25 +216,12 @@ 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.;
+       memset(call->ed, 0, 4 * sizeof(int));
        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];
-               }
+               for (j = 0; j < 4; ++j) call->d[j] += calls[i].d[j], call->ed[j] += calls[i].ed[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;
 }
@@ -264,8 +249,11 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b)
                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]);
+       kputs(";ED4=", &s);
+       for (i = 0; i < 4; ++i) {
+               if (i) kputc(',', &s);
+               kputw(bc->ed[i], &s);
+       }
        kputc('\0', &s);
        // FMT
        kputs("PL", &s); kputc('\0', &s);