* samtools-0.1.10-9 (r844)

 * added the "folded" or reference-free mode for variant calling

diff --git a/bamtk.c b/bamtk.c
index 6d4eb7699b9e02809af110aa1c923f19314e675e..cb1790614a37e157bca560da7c7f5135b8cc267d 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.10-8 (r841)"
+#define PACKAGE_VERSION "0.1.10-9 (r844)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/bcftools/call1.c b/bcftools/call1.c
index b0b14fc5307817cad907ecc6f7126716e80599a5..5e4fc9fbc267928260c678ef3ce62f942fcebc7b 100644 (file)
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -26,6 +26,7 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 #define VC_CALL_GT 2048
 #define VC_ADJLD   4096
 #define VC_NO_INDEL 8192
+#define VC_FOLDED 16384
 
 typedef struct {
        int flag, prior_type, n1;
@@ -216,8 +217,9 @@ int bcfview(int argc, char *argv[])
        tid = begin = end = -1;
        memset(&vc, 0, sizeof(viewconf_t));
        vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.;
-       while ((c = getopt(argc, argv, "N1:l:cHAGvbSuP:t:p:QgLi:I")) >= 0) {
+       while ((c = getopt(argc, argv, "fN1:l:cHAGvbSuP:t:p:QgLi:I")) >= 0) {
                switch (c) {
+               case 'f': vc.flag |= VC_FOLDED; break;
                case '1': vc.n1 = atoi(optarg); break;
                case 'l': vc.fn_list = strdup(optarg); break;
                case 'N': vc.flag |= VC_ACGT_ONLY; break;
@@ -260,6 +262,7 @@ int bcfview(int argc, char *argv[])
                fprintf(stderr, "         -Q        output the QCALL likelihood format\n");
                fprintf(stderr, "         -L        calculate LD for adjacent sites\n");
                fprintf(stderr, "         -I        skip indels\n");
+               fprintf(stderr, "         -f        reference-free variant calling\n");
                fprintf(stderr, "         -1 INT    number of group-1 samples [0]\n");
                fprintf(stderr, "         -l FILE   list of sites to output [all sites]\n");
                fprintf(stderr, "         -t FLOAT  scaled substitution mutation rate [%.4lg]\n", vc.theta);
@@ -293,7 +296,8 @@ int bcfview(int argc, char *argv[])
                        bcf_p1_set_n1(p1, vc.n1);
                        bcf_p1_init_subprior(p1, vc.prior_type, vc.theta);
                }
-               if (vc.indel_frac > 0.) bcf_p1_indel_prior(p1, vc.indel_frac);
+               if (vc.indel_frac > 0.) bcf_p1_indel_prior(p1, vc.indel_frac); // otherwise use the default indel_frac
+               if (vc.flag & VC_FOLDED) bcf_p1_set_folded(p1);
        }
        if (vc.fn_list) hash = bcf_load_pos(vc.fn_list, h);
        if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {

diff --git a/bcftools/prob1.c b/bcftools/prob1.c
index 176a0fc96d4e0b12f14172bc7c0d68297e01a50a..8bf968f6adffd6a7e22058d6c2c5886f33f7a5c1 100644 (file)
--- a/bcftools/prob1.c
+++ b/bcftools/prob1.c
@@ -32,7 +32,7 @@ unsigned char seq_nt4_table[256] = {
 };
 
 struct __bcf_p1aux_t {
-       int n, M, n1, is_indel;
+       int n, M, n1, is_indel, is_folded;
        double *q2p, *pdg; // pdg -> P(D|g)
        double *phi, *phi_indel;
        double *z, *zswap; // aux for afs
@@ -43,6 +43,13 @@ struct __bcf_p1aux_t {
        int PL_len;
 };
 
+static void fold_array(int M, double *x)
+{
+       int k;
+       for (k = 0; k < M/2; ++k)
+               x[k] = x[M-k] = (x[k] + x[M-k]) / 2.;
+}
+
 void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x)
 {
        int i;
@@ -155,6 +162,15 @@ int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
        return 0;
 }
 
+void bcf_p1_set_folded(bcf_p1aux_t *p1a)
+{
+       if (p1a->n1 < 0) {
+               p1a->is_folded = 1;
+               fold_array(p1a->M, p1a->phi);
+               fold_array(p1a->M, p1a->phi_indel);
+       }
+}
+
 void bcf_p1_destroy(bcf_p1aux_t *ma)
 {
        if (ma) {
@@ -373,7 +389,7 @@ int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
        // 
        rst->rank0 = cal_pdg(b, ma);
        rst->f_exp = mc_cal_afs(ma);
-       rst->p_ref = ma->afs1[ma->M];
+       rst->p_ref = ma->is_folded? ma->afs1[ma->M] + ma->afs1[0] : ma->afs1[ma->M];
        // calculate f_flat and f_em
        for (k = 0, sum = 0.; k <= ma->M; ++k)
                sum += (long double)ma->z[k];
@@ -412,6 +428,7 @@ int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
 void bcf_p1_dump_afs(bcf_p1aux_t *ma)
 {
        int k;
+       if (ma->is_folded) fold_array(ma->M, ma->afs);
        fprintf(stderr, "[afs]");
        for (k = 0; k <= ma->M; ++k)
                fprintf(stderr, " %d:%.3lf", k, ma->afs[ma->M - k]);

diff --git a/bcftools/prob1.h b/bcftools/prob1.h
index 6d9d28e3cee6c7d0a66efbd5314912ac511cd384..38275349750bde05f386387a36dc6ffdc0466223 100644 (file)
--- a/bcftools/prob1.h
+++ b/bcftools/prob1.h
@@ -32,6 +32,7 @@ extern "C" {
        int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
        long double bcf_p1_cal_g3(bcf_p1aux_t *p1a, double g[3]);
        int bcf_p1_set_n1(bcf_p1aux_t *b, int n1);
+       void bcf_p1_set_folded(bcf_p1aux_t *p1a); // only effective when set_n1() is not called
 
 #ifdef __cplusplus
 }