* samtools-0.1.8-2 (r617)

 * allele frequency calculation apparently works...

diff --git a/bam_mcns.c b/bam_mcns.c
index 845dfcda5a956305c66b3b5d51ceaff4204b803b..b69ec0f0abaceb6aa0408cb61a9adc51b0626765 100644 (file)
--- a/bam_mcns.c
+++ b/bam_mcns.c
@@ -2,7 +2,7 @@
 #include <stdlib.h>
 #include "bam_mcns.h"
 
-#define MC_MIN_QUAL 20
+#define MC_MIN_QUAL 13
 #define MC_MAX_SUMQ 3000
 #define MC_MAX_SUMQP 1e-300
 
@@ -10,7 +10,7 @@ struct __mc_aux_t {
        int n, N;
        int ref, alt;
        double *q2p, *pdg; // pdg -> P(D|g)
-       int *qsum, *bcnt;
+       int *qsum, *bcnt, rcnt[4];
 };
 
 mc_aux_t *mc_init(int n) // FIXME: assuming diploid
@@ -42,10 +42,12 @@ static void sum_err(int *n, const bam_pileup1_t **plp, mc_aux_t *ma)
        int i, j;
        memset(ma->qsum, 0, sizeof(int) * 4 * ma->n);
        memset(ma->bcnt, 0, sizeof(int) * 4 * ma->n);
+       memset(ma->rcnt, 0, sizeof(int) * 4);
        for (j = 0; j < ma->n; ++j) {
-               int *qsum = ma->qsum + j * 4;
+               int tmp, *qsum = ma->qsum + j * 4;
                int *bcnt = ma->bcnt + j * 4;
-               for (i = 0; i < n[j]; ++i) {
+               double r = drand48(), rr;
+               for (i = tmp = 0; i < n[j]; ++i) {
                        const bam_pileup1_t *p = plp[j] + i;
                        int q, b;
                        if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue;
@@ -56,6 +58,14 @@ static void sum_err(int *n, const bam_pileup1_t **plp, mc_aux_t *ma)
                        if (b > 3) continue; // N
                        qsum[b] += q;
                        ++bcnt[b];
+                       ++tmp;
+               }
+               if (tmp) {
+                       for (i = 0, rr = 0.; i < 4; ++i) {
+                               rr += (double)bcnt[i] / tmp;
+                               if (rr >= r) break;
+                       }
+                       if (i < 4) ++ma->rcnt[i];
                }
        }
 }
@@ -85,17 +95,17 @@ static void cal_pdg(mc_aux_t *ma)
                qsum = ma->qsum + j * 4;
                bcnt = ma->bcnt + j * 4;
                pi[1] = 3 * (bcnt[ma->ref] + bcnt[ma->alt]);
-               pi[0] = qsum[ma->alt];
-               pi[2] = qsum[ma->ref];
+               pi[0] = qsum[ma->ref];
+               pi[2] = qsum[ma->alt];
                for (i = 0; i < 3; ++i)
-                       pdg[i] = pi[i] < MC_MAX_SUMQ? MC_MAX_SUMQP : ma->q2p[pi[i]];
+                       pdg[i] = pi[i] > MC_MAX_SUMQ? MC_MAX_SUMQP : ma->q2p[pi[i]];
        }
 }
 
 double mc_freq0(int ref, int *n, const bam_pileup1_t **plp, mc_aux_t *ma, int *_ref, int *alt)
 {
        int i, acnt[4], j;
-       double f0;
+       double fr = -1., f0 = -1.;
        sum_err(n, plp, ma);
        set_allele(ref, ma);
        cal_pdg(ma);
@@ -103,17 +113,19 @@ double mc_freq0(int ref, int *n, const bam_pileup1_t **plp, mc_aux_t *ma, int *_
        for (i = 0; i < ma->n; ++i)
                for (j = 0; j < 4; ++j)
                        acnt[j] += ma->bcnt[i * 4 + j];
-       f0 = acnt[ma->ref] + acnt[ma->alt] == 0? -1.
-               : (double)acnt[ref] / (acnt[ma->ref] + acnt[ma->alt]);
+       if (ma->rcnt[ma->ref] + ma->rcnt[ma->alt]) // never used...
+               fr = (double)ma->rcnt[ref] / (ma->rcnt[ma->ref] + ma->rcnt[ma->alt]);
+       if (acnt[ma->ref] + acnt[ma->alt])
+               f0 = (double)acnt[ref] / (acnt[ma->ref] + acnt[ma->alt]);
        *_ref = ma->ref; *alt = ma->alt;
-       return f0;
+       return ma->n == 1 || fr < 0.? f0 : fr;
 }
 
 double mc_freq_iter(double f0, mc_aux_t *ma)
 {
        double f, f3[3];
        int i, j;
-       f3[0] = f0*f0; f3[1] = 2.*f0*(1.-f0); f3[2] = (1.-f0)*(1.-f0);
+       f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
        for (i = 0, f = 0.; i < ma->n; ++i) {
                double up, dn, *pdg;
                pdg = ma->pdg + i * 3;
@@ -123,5 +135,6 @@ double mc_freq_iter(double f0, mc_aux_t *ma)
                        dn += pdg[j] * f3[j];
                f += up / dn;
        }
+       f /= ma->n * 2.;
        return f;
 }

diff --git a/bam_plcmd.c b/bam_plcmd.c
index e4de8332b69c9218db1be387f6018f05fc2d4bc4..708e63e7e8b600baf166e23979990711d9bf5829 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -548,16 +548,26 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        ref_tid = tid;
                }
                if (conf->vcf) {
-                       double f;
-                       int j, _ref, _alt, _ref0, depth, rms_q;
+                       double f0, f; // the reference allele frequency
+                       int j, _ref, _alt, _ref0, depth, rms_q, _ref0b;
                        uint64_t sqr_sum;
-                       _ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
+                       _ref0 = _ref0b = (ref && pos < ref_len)? ref[pos] : 'N';
                        _ref0 = bam_nt16_nt4_table[bam_nt16_table[_ref0]];
-                       f = mc_freq0(_ref0, n_plp, plp, ma, &_ref, &_alt);
-                       printf("%s\t%d\t.\t%c\t", h->target_name[tid], pos + 1, "ACGTN"[_ref0]);
+                       f = f0 = mc_freq0(_ref0, n_plp, plp, ma, &_ref, &_alt);
+                       if (f >= 0.0) {
+                               double flast = f;
+                               for (j = 0; j < 10; ++j) {
+                                       f = mc_freq_iter(flast, ma);
+                                       if (fabs(f - flast) < 1e-3) break;
+                                       flast = f;
+                               }
+                       }
+                       printf("%s\t%d\t.\t%c\t", h->target_name[tid], pos + 1, _ref0b);
                        if (_ref0 == _ref) putchar("ACGTN"[_alt]);
                        else printf("%c,%c", "ACGTN"[_ref], "ACGTN"[_alt]);
-                       printf("\t0\tPASS\t"); // FIXME: currently these not available
+                       printf("\t0\t"); // FIXME: currently these not available
+                       if (f0 < 0.) printf("Q13\t");
+                       else printf(".\t");
                        for (i = depth = 0, sqr_sum = 0; i < n; ++i) {
                                depth += n_plp[i];
                                for (j = 0; j < n_plp[i]; ++j) {
@@ -567,7 +577,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                                }
                        }
                        rms_q = (int)(sqrt((double)sqr_sum / depth) + .499);
-                       printf("DP=%d;MQ=%d;AF=%.3lg", depth, rms_q, 1.-f); // FIXME: not working for triallelic alleles
+                       printf("DP=%d;MQ=%d;AF=%.3lg", depth, rms_q, f0<0.?0.:1.-f);
                        printf("\tDP");
                        // output genotype information; FIXME: to be implmented...
                        for (i = 0; i < n; ++i)

diff --git a/bamtk.c b/bamtk.c
index f93cf524c3ef8ec6eda5e76d2929802801437f9e..b5f6b670ebbff83dae88973c8f8bba14ba19fc91 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.8-1 (r615)"
+#define PACKAGE_VERSION "0.1.8-2 (r617)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);