* samtools-0.1.8-3 (r627)

 * multi-sample snp calling appears to work. More tests needed.

diff --git a/bam_mcns.c b/bam_mcns.c
index cd64b0ac139814706632a05d2e7b75d619a36b8a..dee2016507100888faf053163ec47a8b8b474828 100644 (file)
--- a/bam_mcns.c
+++ b/bam_mcns.c
@@ -12,7 +12,7 @@ struct __mc_aux_t {
        double theta;
        double *q2p, *pdg; // pdg -> P(D|g)
        double *alpha, *beta;
-       int *qsum, *bcnt, rcnt[4];
+       int *qsum, *bcnt;
 };
 
 void mc_init_prior(mc_aux_t *ma, double theta)
@@ -65,11 +65,9 @@ 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 tmp, *qsum = ma->qsum + j * 4;
                int *bcnt = ma->bcnt + j * 4;
-               double r = drand48(), rr;
                for (i = tmp = 0; i < n[j]; ++i) {
                        const bam_pileup1_t *p = plp[j] + i;
                        int q, b;
@@ -83,13 +81,6 @@ static void sum_err(int *n, const bam_pileup1_t **plp, mc_aux_t *ma)
                        ++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];
-               }
        }
 }
 
@@ -127,21 +118,21 @@ static void cal_pdg(mc_aux_t *ma)
 // return the reference allele frequency
 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 fr = -1., f0 = -1.;
+       int i, cnt;
+       double f;
        sum_err(n, plp, ma);
        set_allele(ref, ma);
        cal_pdg(ma);
-       acnt[0] = acnt[1] = acnt[2] = acnt[3] = 0;
-       for (i = 0; i < ma->n; ++i)
-               for (j = 0; j < 4; ++j)
-                       acnt[j] += ma->bcnt[i * 4 + j];
-       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 ma->n == 1 || fr < 0.? f0 : fr;
+       for (i = cnt = 0, f = 0.; i < ma->n; ++i) {
+               int *bcnt = ma->bcnt + i * 4;
+               int x = bcnt[ma->ref] + bcnt[ma->alt];
+               if (x) {
+                       ++cnt;
+                       f += (double)bcnt[ma->ref] / x;
+               }
+       }
+       return f / cnt;
 }
 // f0 is the reference allele frequency
 double mc_freq_iter(double f0, mc_aux_t *ma)

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 285477050d19f489d7be34722846eca8e6407e14..2afebeadf85bc2ee020e3c8aecd0209dccebc51d 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -557,11 +557,13 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        f = f0 = mc_freq0(_ref0, n_plp, plp, ma, &_ref, &_alt);
                        if (f >= 0.0) {
                                double q, flast = f;
-                               for (j = 0; j < 10; ++j){
+                               for (j = 0; j < 10; ++j) {
                                        f = mc_freq_iter(flast, ma);
+//                                     printf("%lg->%lg\n", flast, f);
                                        if (fabs(f - flast) < 1e-3) break;
                                        flast = f;
                                }
+                               if (1. - f < 1e-4) f = 1.;
                                pref = mc_ref_prob(ma);
                                is_var = (pref < .5);
                                q = is_var? pref : 1. - pref;
@@ -655,7 +657,17 @@ int bam_mpileup(int argc, char *argv[])
                }
        }
        if (argc == 1) {
-               fprintf(stderr, "Usage: samtools mpileup [-r reg] [-f in.fa] [-l pos] in1.bam [in2.bam [...]]\n");
+               fprintf(stderr, "\n");
+               fprintf(stderr, "Usage:   samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
+               fprintf(stderr, "Options: -f FILE     reference sequence file [null]\n");
+               fprintf(stderr, "         -r STR      region in which pileup is generated [null]\n");
+               fprintf(stderr, "         -l FILE     list of positions (format: chr pos) [null]\n");
+               fprintf(stderr, "         -M INT      cap mapping quality at INT [%d]\n", mplp.max_mq);
+               fprintf(stderr, "         -q INT      filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
+               fprintf(stderr, "         -V          generate VCF output (SNP calling)\n");
+               fprintf(stderr, "         -v          show variant sites only\n");
+               fprintf(stderr, "\n");
+               fprintf(stderr, "Notes: Assuming error independency and diploid individuals.\n\n");
                return 1;
        }
        mpileup(&mplp, argc - optind, argv + optind);

diff --git a/bamtk.c b/bamtk.c
index b5f6b670ebbff83dae88973c8f8bba14ba19fc91..b51df96501415599e114cec3ac06353ff539de1b 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.8-2 (r617)"
+#define PACKAGE_VERSION "0.1.8-3 (r627)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);