Imported Upstream version 0.1.11

[samtools.git] / bcftools / call1.c

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)) {