finished VCF->BCF conversion

[samtools.git] / bcftools / call1.c

diff --git a/bcftools/call1.c b/bcftools/call1.c
index 809fe344bfd0a7abf822b82db3670c25ed47689c..286c0141856f0f7f2bac22f4e7f8ab80f52afa2c 100644 (file)
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -30,7 +30,7 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 
 typedef struct {
        int flag, prior_type, n1, n_sub, *sublist;
-       char *fn_list, *prior_file, **subsam;
+       char *fn_list, *prior_file, **subsam, *fn_dict;
        double theta, pref, indel_frac;
 } viewconf_t;
 
@@ -208,8 +208,10 @@ static char **read_samples(const char *fn, int *_n)
        kstring_t s;
        int dret, n = 0, max = 0;
        char **sam = 0;
+       *_n = 0;
        s.l = s.m = 0; s.s = 0;
        fp = gzopen(fn, "r");
+       if (fp == 0) return 0; // fail to open file
        ks = ks_init(fp);
        while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
                if (max == n) {
@@ -245,7 +247,7 @@ static void write_header(bcf_hdr_t *h)
        if (!strstr(str.s, "##INFO=<ID=PV4,"))
                kputs("##INFO=<ID=PV4,Number=4,Type=Float,Description=\"P-values for strand bias, baseQ bias, mapQ bias and tail distance bias\">\n", &str);
     if (!strstr(str.s, "##INFO=<ID=INDEL,"))
-        kputs("##INFO=<ID=INDEL,Number=0,Type=Flag,Descriptin=\"Indicates that the variant is an INDEL.\">\n", &str);
+        kputs("##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">\n", &str);
     if (!strstr(str.s, "##INFO=<ID=GT,"))
         kputs("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n", &str);
     if (!strstr(str.s, "##FORMAT=<ID=GQ,"))
@@ -284,10 +286,11 @@ int bcfview(int argc, char *argv[])
        memset(&vc, 0, sizeof(viewconf_t));
        vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.;
        vc.n_sub = 0; vc.subsam = 0; vc.sublist = 0;
-       while ((c = getopt(argc, argv, "N1:l:cHAGvbSuP:t:p:QgLi:IMs:")) >= 0) {
+       while ((c = getopt(argc, argv, "N1:l:cHAGvbSuP:t:p:QgLi:IMs:D:")) >= 0) {
                switch (c) {
                case '1': vc.n1 = atoi(optarg); break;
                case 'l': vc.fn_list = strdup(optarg); break;
+               case 'D': vc.fn_dict = strdup(optarg); break;
                case 'N': vc.flag |= VC_ACGT_ONLY; break;
                case 'G': vc.flag |= VC_NO_GENO; break;
                case 'A': vc.flag |= VC_KEEPALT; break;
@@ -330,6 +333,7 @@ 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, "         -D FILE   sequence dictionary for VCF->BCF conversion [null]\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 [%.4g]\n", vc.theta);
@@ -341,6 +345,10 @@ int bcfview(int argc, char *argv[])
                return 1;
        }
 
+       if ((vc.flag & VC_VCFIN) && (vc.flag & VC_BCFOUT) && vc.fn_dict == 0) {
+               fprintf(stderr, "[%s] For VCF->BCF conversion please specify the sequence dictionary with -D\n", __func__);
+               return 1;
+       }
        b = calloc(1, sizeof(bcf1_t));
        blast = calloc(1, sizeof(bcf1_t));
        strcpy(moder, "r");
@@ -350,6 +358,8 @@ int bcfview(int argc, char *argv[])
        if (vc.flag & VC_UNCOMP) strcat(modew, "u");
        bp = vcf_open(argv[optind], moder);
        hin = hout = vcf_hdr_read(bp);
+       if (vc.fn_dict && (vc.flag & VC_VCFIN))
+               vcf_dictread(bp, hin, vc.fn_dict);
        bout = vcf_open("-", modew);
        if (!(vc.flag & VC_QCALL)) {
                if (vc.n_sub) {
@@ -460,6 +470,7 @@ int bcfview(int argc, char *argv[])
        vcf_close(bp); vcf_close(bout);
        if (hash) kh_destroy(set64, hash);
        if (vc.fn_list) free(vc.fn_list);
+       if (vc.fn_dict) free(vc.fn_dict);
        if (vc.n_sub) {
                int i;
                for (i = 0; i < vc.n_sub; ++i) free(vc.subsam[i]);