* samtools-0.1.10-9 (r844)

[samtools.git] / bcftools / call1.c

diff --git a/bcftools/call1.c b/bcftools/call1.c
index 15f6f8bcc7095c37ea5fb589efdce630680b07b7..5e4fc9fbc267928260c678ef3ce62f942fcebc7b 100644 (file)
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -25,6 +25,8 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 #define VC_QCALL   1024
 #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;
@@ -215,8 +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:")) >= 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;
@@ -229,6 +232,7 @@ int bcfview(int argc, char *argv[])
                case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
                case 'H': vc.flag |= VC_HWE; break;
                case 'g': vc.flag |= VC_CALL_GT | VC_CALL; break;
+               case 'I': vc.flag |= VC_NO_INDEL; break;
                case 't': vc.theta = atof(optarg); break;
                case 'p': vc.pref = atof(optarg); break;
                case 'i': vc.indel_frac = atof(optarg); break;
@@ -257,6 +261,8 @@ int bcfview(int argc, char *argv[])
                fprintf(stderr, "         -N        skip sites where REF is not A/C/G/T\n");
                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);
@@ -290,7 +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)) {
@@ -311,7 +318,9 @@ int bcfview(int argc, char *argv[])
                }
        }
        while (vcf_read(bp, h, b) > 0) {
-               if (vc.flag & VC_ACGT_ONLY) {
+               int is_indel = bcf_is_indel(b);
+               if ((vc.flag & VC_NO_INDEL) && is_indel) continue;
+               if ((vc.flag & VC_ACGT_ONLY) && !is_indel) {
                        int x;
                        if (b->ref[0] == 0 || b->ref[1] != 0) continue;
                        x = toupper(b->ref[0]);