* samtools-0.1.8-2 (r617)

[samtools.git] / bam_plcmd.c

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)