* samtools-0.1.8-6 (r638)

 * skip isnan/isinf in case of float underflow
 * added the flat prior
 * fixed an issue where there are no reads supporting the reference

diff --git a/bam_mcns.c b/bam_mcns.c
index d337e5a290aa76a1f1faa2c8a687db4639962a16..7ef9f0f44702d9f6e4b499681f328ffe594b5afd 100644 (file)
--- a/bam_mcns.c
+++ b/bam_mcns.c
@@ -12,7 +12,7 @@
 
 struct __mc_aux_t {
        int n, M;
-       int ref, alt;
+       int ref, alt, alt2;
        double *q2p, *pdg; // pdg -> P(D|g)
        double *alpha, *beta;
        double *z, *zswap; // aux for afs
@@ -26,6 +26,9 @@ void mc_init_prior(mc_aux_t *ma, int type, double theta)
        if (type == MC_PTYPE_COND2) {
                for (i = 0; i <= 2 * ma->n; ++i)
                        ma->alpha[i] = 2. * (i + 1) / (2 * ma->n + 1) / (2 * ma->n + 2);
+       } else if (type == MC_PTYPE_FLAT) {
+               for (i = 0; i <= ma->M; ++i)
+                       ma->alpha[i] = 1. / (ma->M + 1);
        } else {
                double sum;
                for (i = 0, sum = 0.; i < 2 * ma->n; ++i)
@@ -111,9 +114,11 @@ static void set_allele(int ref, mc_aux_t *ma)
        for (i = 1; i < 4; ++i) // insertion sort
                for (j = i; j > 0 && sum[j] < sum[j-1]; --j)
                        tmp = sum[j], sum[j] = sum[j-1], sum[j-1] = tmp;
-       ma->ref = sum[3]&3; ma->alt = sum[2]&3;
-       if (ref == ma->alt) tmp = ma->ref, ma->ref = ma->alt, ma->alt = tmp;
-       // note that ma->ref might not be ref in case of triallele
+       ma->ref = sum[3]&3; ma->alt = sum[2]&3; ma->alt2 = -1;
+       if (ma->ref != ref) {
+               if (ma->alt == ref) tmp = ma->ref, ma->ref = ma->alt, ma->alt = tmp;
+               else ma->alt2 = ma->alt, ma->alt = ma->ref, ma->ref = ref;
+       }
 }
 
 static void cal_pdg(mc_aux_t *ma)
@@ -248,11 +253,14 @@ static void mc_add_afs(mc_aux_t *ma, double PD, double *f_map, double *p_map)
        int k, l;
        double sum = 0.;
        memset(ma->afs1, 0, sizeof(double) * (2 * ma->n + 1));
+       *f_map = *p_map = -1.;
        for (k = 0; k <= 2 * ma->n; ++k) {
                mc_cal_z(ma, k);
                for (l = 0; l <= 2 * ma->n; ++l)
                        ma->afs1[l] += ma->alpha[k] * ma->z[l] / PD;
        }
+       for (k = 0; k <= ma->M; ++k)
+               if (isnan(ma->afs1[k]) || isinf(ma->afs1[k])) return;
        for (k = 0; k <= 2 * ma->n; ++k) {
                ma->afs[k] += ma->afs1[k];
                sum += ma->afs1[k];
@@ -280,7 +288,7 @@ int mc_cal(int ref, int *n, const bam_pileup1_t **plp, mc_aux_t *ma, mc_rst_t *r
        set_allele(ref, ma);
        cal_pdg(ma);
        // set ref/major allele
-       rst->ref = ma->ref; rst->alt = ma->alt;
+       rst->ref = ma->ref; rst->alt = ma->alt; rst->alt2 = ma->alt2;
        // calculate naive and Nielsen's freq
        rst->f_naive = mc_freq0(ma, &rst->f_nielsen);
        { // calculate f_em

diff --git a/bam_mcns.h b/bam_mcns.h
index 5c7c42026def5133b2468e882785d756dfaee750..0781975361a732ecf8ec285948832e4458d3e0a4 100644 (file)
--- a/bam_mcns.h
+++ b/bam_mcns.h
@@ -8,7 +8,7 @@ typedef struct __mc_aux_t mc_aux_t;
 
 typedef struct {
        // O(n)
-       int ref, alt;
+       int ref, alt, alt2;
        double f_em, f_naive, f_nielsen;
        // O(n^2)
        double PD, p_ref, f_exp;
@@ -18,6 +18,7 @@ typedef struct {
 
 #define MC_PTYPE_FULL  1
 #define MC_PTYPE_COND2 2
+#define MC_PTYPE_FLAT  3
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 195a59602ab4e778084b6eefc105ee1d608643bb..a1c87ab6f67831fe4f949a4625f5cd685b72317d 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -584,8 +584,8 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        ++N; // number of processed lines
                        printf("%s\t%d\t.\t%c\t", h->target_name[tid], pos + 1, _ref0b);
                        if (is_var) {
-                               if (_ref0 == r.ref) putchar("ACGTN"[r.alt]);
-                               else printf("%c,%c", "ACGTN"[r.ref], "ACGTN"[r.alt]);
+                               putchar("ACGTN"[r.alt]);
+                               if (r.alt2 >= 0 && r.alt2 < 4) printf(",%c", "ACGT"[r.alt2]);
                        } else putchar('.');
                        printf("\t%d\t", qref);
                        if (!tot) printf("Q13\t");
@@ -665,10 +665,18 @@ int bam_mpileup(int argc, char *argv[])
        mplp.max_mq = 60;
        mplp.prior_type = MC_PTYPE_FULL;
        mplp.theta = 1e-3;
-       while ((c = getopt(argc, argv, "vVcF2Sf:r:l:VM:q:t:")) >= 0) {
+       while ((c = getopt(argc, argv, "vVcFSP:f:r:l:VM:q:t:")) >= 0) {
                switch (c) {
                case 't': mplp.theta = atof(optarg); break;
-               case '2': mplp.prior_type = MC_PTYPE_COND2; break;
+               case 'P':
+                       if (strcmp(optarg, "full") == 0) mplp.prior_type = MC_PTYPE_FULL;
+                       else if (strcmp(optarg, "cond2") == 0) mplp.prior_type = MC_PTYPE_COND2;
+                       else if (strcmp(optarg, "flat") == 0) mplp.prior_type = MC_PTYPE_FLAT;
+                       else {
+                               fprintf(stderr, "[%s] unrecognized prior type.\n", __func__);
+                               return 1;
+                       }
+                       break;
                case 'f':
                        mplp.fai = fai_load(optarg);
                        if (mplp.fai == 0) return 1;
@@ -693,10 +701,10 @@ int bam_mpileup(int argc, char *argv[])
                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, "         -t FLOAT    scaled mutation rate [%lg]\n", mplp.theta);
+               fprintf(stderr, "         -P STR      prior: full, flat, cond2 [full]");
                fprintf(stderr, "         -c          generate VCF output (consensus calling)\n");
                fprintf(stderr, "         -v          show variant sites only\n");
                fprintf(stderr, "         -S          calculate AFS (slow, to stderr)\n");
-               fprintf(stderr, "         -2          conditional prior\n");
                fprintf(stderr, "\n");
                fprintf(stderr, "Notes: Assuming error independency and diploid individuals.\n\n");
                return 1;

diff --git a/bamtk.c b/bamtk.c
index ae972d54598ecee1fdd7102e36712192d6ae6178..e80d04224f08cf48a37b824b982f8c0134f580bd 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.8-5 (r636)"
+#define PACKAGE_VERSION "0.1.8-6 (r638)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);