* preliminary multisample SNP caller.

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 708e63e7e8b600baf166e23979990711d9bf5829..285477050d19f489d7be34722846eca8e6407e14 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -450,7 +450,7 @@ int bam_pileup(int argc, char *argv[])
  ***********/
 
 typedef struct {
-       int vcf, max_mq, min_mq;
+       int vcf, max_mq, min_mq, var_only;
        char *reg, *fn_pos;
        faidx_t *fai;
        kh_64_t *hash;
@@ -520,6 +520,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
        if (conf->vcf) {
                kstring_t s;
                s.l = s.m = 0; s.s = 0;
+               puts("##fileformat=VCFv4.0");
                kputs("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT", &s);
                for (i = 0; i < n; ++i) {
                        const char *p;
@@ -548,24 +549,33 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        ref_tid = tid;
                }
                if (conf->vcf) {
-                       double f0, f; // the reference allele frequency
-                       int j, _ref, _alt, _ref0, depth, rms_q, _ref0b;
+                       double f0, f, pref = -1.0; // the reference allele frequency
+                       int j, _ref, _alt, _ref0, depth, rms_q, _ref0b, is_var = 0, qref = 0;
                        uint64_t sqr_sum;
                        _ref0 = _ref0b = (ref && pos < ref_len)? ref[pos] : 'N';
                        _ref0 = bam_nt16_nt4_table[bam_nt16_table[_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) {
+                               double q, flast = f;
+                               for (j = 0; j < 10; ++j){
                                        f = mc_freq_iter(flast, ma);
                                        if (fabs(f - flast) < 1e-3) break;
                                        flast = f;
                                }
+                               pref = mc_ref_prob(ma);
+                               is_var = (pref < .5);
+                               q = is_var? pref : 1. - pref;
+                               if (q < 1e-308) q = 1e-308;
+                               qref = (int)(-3.434 * log(q) + .499);
+                               if (qref > 99) qref = 99;
                        }
+                       if (conf->var_only && !is_var) continue;
                        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\t"); // FIXME: currently these not available
+                       if (is_var) {
+                               if (_ref0 == _ref) putchar("ACGTN"[_alt]);
+                               else printf("%c,%c", "ACGTN"[_ref], "ACGTN"[_alt]);
+                       } else putchar('.');
+                       printf("\t%d\t", qref);
                        if (f0 < 0.) printf("Q13\t");
                        else printf(".\t");
                        for (i = depth = 0, sqr_sum = 0; i < n; ++i) {
@@ -578,10 +588,12 @@ 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, f0<0.?0.:1.-f);
-                       printf("\tDP");
+                       printf("\tGT:GQ:DP");
                        // output genotype information; FIXME: to be implmented...
-                       for (i = 0; i < n; ++i)
-                               printf("\t%d", n_plp[i]);
+                       for (i = 0; i < n; ++i) {
+                               int x = mc_call_gt(ma, f, i);
+                               printf("\t%c/%c:%d:%d", "10"[((x&3)==2)], "10"[((x&3)>0)], x>>2, n_plp[i]);
+                       }
                        putchar('\n');
                } else {
                        printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
@@ -628,7 +640,7 @@ int bam_mpileup(int argc, char *argv[])
        mplp_conf_t mplp;
        memset(&mplp, 0, sizeof(mplp_conf_t));
        mplp.max_mq = 60;
-       while ((c = getopt(argc, argv, "f:r:l:VM:q:")) >= 0) {
+       while ((c = getopt(argc, argv, "f:r:l:VvM:q:")) >= 0) {
                switch (c) {
                case 'f':
                        mplp.fai = fai_load(optarg);
@@ -636,6 +648,7 @@ int bam_mpileup(int argc, char *argv[])
                        break;
                case 'r': mplp.reg = strdup(optarg); break;
                case 'l': mplp.fn_pos = strdup(optarg); break;
+               case 'v': mplp.var_only = 1; break;
                case 'V': mplp.vcf = 1; break;
                case 'M': mplp.max_mq = atoi(optarg); break;
                case 'q': mplp.min_mq = atoi(optarg); break;