int main_vcfview(int argc, char *argv[])
{
int c, clevel = -1, in_type = FT_BCF, out_type = FT_VCF;
char *fname_out = NULL, moder[8], modew[8];
while ((c = getopt(argc, argv, "l:bvo:n:z?hu")) >= 0) {
switch (c) {
case 'o':
switch (optarg[0]) {
case 'b': out_type = FT_BCF_GZ; break;
case 'u': out_type = FT_BCF; break;
case 'z': out_type = FT_VCF_GZ; break;
case 'v': out_type = FT_VCF; break;
default: error("The output type \"%s\" not recognised\n", optarg);
}
break;
case 'l': clevel = atoi(optarg); out_type |= FT_GZ; break;
case 'v': in_type = FT_VCF; break;
case 'b': out_type = FT_BCF_GZ; break;
case 'u': out_type = FT_BCF; break;
case 'z': out_type = FT_VCF_GZ; break;
case 'n': fname_out = optarg; break;
case '?':
case 'h': usage(); return 1; break;
}
}
if (argc!=optind+1) { usage(); return 1; }
// Init reader
strcpy(moder, "r");
if ( (!strcmp("-",argv[optind]) && (in_type & FT_BCF)) || (hts_file_type(argv[optind]) & FT_BCF)) strcat(moder, "b");
htsFile *fp_in = hts_open(argv[optind], moder, NULL);
if ( !fp_in ) error("Fail to open: %s\n", argv[optind]);
bcf_hdr_t *hdr = vcf_hdr_read(fp_in);
if ( !hdr ) error("Fail to read VCF/BCF header: %s\n", argv[optind]);
bcf1_t *rec = bcf_init1();
// Init writer
strcpy(modew, "w");
if (clevel >= 0 && clevel <= 9) sprintf(modew + 1, "%d", clevel);
if (out_type & FT_GZ) strcat(modew,"z");
if (out_type & FT_BCF) strcat(modew, "b");
if (out_type == FT_BCF) strcat(modew, "u"); // uncompressed BCF output
htsFile *fp_out = hts_open(fname_out ? fname_out : "-", modew, NULL);
vcf_hdr_write(fp_out, hdr);
while ( vcf_read1(fp_in, hdr, rec) >= 0) vcf_write1(fp_out, hdr, rec);
bcf_destroy1(rec);
bcf_hdr_destroy(hdr);
hts_close(fp_in);
hts_close(fp_out);
return 0;
}
int main_vcfview(int argc, char *argv[])
{
int i, c, clevel = -1, flag = 0, n_samples = -1, *imap = 0, excl_snp = 0, excl_indel = 0;
char *fn_ref = 0, *fn_out = 0, moder[8], **samples = 0;
bcf_hdr_t *h, *hsub = 0;
htsFile *in;
bcf1_t *b;
while ((c = getopt(argc, argv, "l:bSt:o:T:s:GNI")) >= 0) {
switch (c) {
case 'l': clevel = atoi(optarg); flag |= 2; break;
case 'S': flag |= 1; break;
case 'b': flag |= 2; break;
case 'G': n_samples = 0; break;
case 't': fn_ref = optarg; flag |= 1; break;
case 'o': fn_out = optarg; break;
case 's': samples = hts_readlines(optarg, &n_samples); break;
case 'N': excl_snp = 1; break;
case 'I': excl_indel = 1; break;
}
}
if (argc == optind) {
fprintf(stderr, "\nUsage: vcfview [options] <in.bcf>|<in.vcf>|<in.vcf.gz>\n\n");
fprintf(stderr, "Options: -b output in BCF\n");
fprintf(stderr, " -S input is VCF\n");
fprintf(stderr, " -o FILE output file name [stdout]\n");
fprintf(stderr, " -l INT compression level [%d]\n", clevel);
fprintf(stderr, " -t FILE list of reference names and lengths [null]\n");
fprintf(stderr, " -s FILE/STR list of samples (STR if started with ':'; FILE otherwise) [null]\n");
fprintf(stderr, " -G drop individual genotype information\n");
fprintf(stderr, " -N exclude SNPs\n");
fprintf(stderr, " -I exclude INDELs\n");
fprintf(stderr, "\n");
return 1;
}
strcpy(moder, "r");
if ((flag&1) == 0 && !(file_type(argv[optind])&(IS_VCF|IS_VCF_GZ))) strcat(moder, "b");
in = hts_open(argv[optind], moder, fn_ref);
h = vcf_hdr_read(in);
if (h == 0) {
fprintf(stderr, "[E::%s] fail to read the VCF/BCF2 header\n", __func__);
hts_close(in);
return 1;
}
if (n_samples >= 0) {
if (n_samples) imap = (int*)malloc(n_samples * sizeof(int));
hsub = bcf_hdr_subset(h, n_samples, samples, imap);
}
b = bcf_init1();
if ((flag&4) == 0) { // VCF/BCF output
htsFile *out;
char modew[8];
strcpy(modew, "w");
if (clevel >= 0 && clevel <= 9) sprintf(modew + 1, "%d", clevel);
if (flag&2) strcat(modew, "b");
out = hts_open(fn_out? fn_out : "-", modew, 0);
vcf_hdr_write(out, hsub? hsub : h);
if (optind + 1 < argc && !(flag&1)) { // BAM input and has a region
hts_idx_t *idx;
if ((idx = bcf_index_load(argv[optind])) == 0) {
fprintf(stderr, "[E::%s] fail to load the BCF index\n", __func__);
return 1;
}
for (i = optind + 1; i < argc; ++i) {
hts_itr_t *iter;
if ((iter = bcf_itr_querys(idx, h, argv[i])) == 0) {
fprintf(stderr, "[E::%s] fail to parse region '%s'\n", __func__, argv[i]);
continue;
}
while (bcf_itr_next((BGZF*)in->fp, iter, b) >= 0) {
if (excl_snp && bcf_is_snp(b)) continue;
if (excl_indel && !bcf_is_snp(b)) continue;
if (n_samples >= 0) {
bcf_subset(h, b, n_samples, imap);
vcf_write1(out, hsub, b);
} else vcf_write1(out, h, b);
}
hts_itr_destroy(iter);
}
hts_idx_destroy(idx);
} else {
while (vcf_read1(in, h, b) >= 0) {
if (excl_snp && bcf_is_snp(b)) continue;
if (excl_indel && !bcf_is_snp(b)) continue;
if (n_samples >= 0) {
bcf_subset(h, b, n_samples, imap);
vcf_write1(out, hsub, b);
} else vcf_write1(out, h, b);
}
}
hts_close(out);
}
bcf_destroy1(b);
if (n_samples > 0) {
for (i = 0; i < n_samples; ++i) free(samples[i]);
free(samples);
bcf_hdr_destroy(hsub);
free(imap);
}
bcf_hdr_destroy(h);
hts_close(in);
return 0;
}
int main_view(int argc, char *argv[])
{
int i, c, n_files = 0, out_bcf = 0, clevel = -1, multi_flag = 0, excl = 0, not_vcf = 0, in_mem = 0, u_set = 0;
long seekn = -1, n_rec = LONG_MAX, n_read = 0;
bgtm_t *bm = 0;
bcf1_t *b;
htsFile *out = 0;
char modew[8], *reg = 0, *site_flt = 0;
void *bed = 0;
int n_groups = 0;
char *gexpr[BGT_MAX_GROUPS], *aexpr = 0, *dbfn = 0, *fmt = 0;
bgt_file_t **files = 0;
fmf_t *vardb = 0;
while ((c = getopt(argc, argv, "ubs:r:l:CMGB:ef:g:a:i:n:SHt:d:")) >= 0) {
if (c == 'b') out_bcf = 1;
else if (c == 'r') reg = optarg;
else if (c == 'l') clevel = atoi(optarg);
else if (c == 'e') excl = 1;
else if (c == 'u') u_set = 1;
else if (c == 'B') bed = bed_read(optarg);
else if (c == 'C') multi_flag |= BGT_F_SET_AC;
else if (c == 'G') multi_flag |= BGT_F_NO_GT;
else if (c == 'S') multi_flag |= BGT_F_NO_GT | BGT_F_CNT_AL, not_vcf = 1;
else if (c == 'H') multi_flag |= BGT_F_NO_GT | BGT_F_CNT_HAP, not_vcf = 1;
else if (c == 'M') in_mem = 1;
else if (c == 'i') seekn = atol(optarg) - 1;
else if (c == 'n') n_rec = atol(optarg);
else if (c == 'f') site_flt = optarg;
else if (c == 't') fmt = optarg, not_vcf = 1;
else if (c == 'd') dbfn = optarg;
else if (c == 's' && n_groups < BGT_MAX_GROUPS) gexpr[n_groups++] = optarg;
else if (c == 'a') aexpr = optarg;
}
if (n_rec < 0) {
fprintf(stderr, "[E::%s] option -n must be at least 0.\n", __func__);
return 1;
}
if (clevel > 9) clevel = 9;
if (u_set) clevel = 0, out_bcf = 1;
if (n_groups > 1) multi_flag |= BGT_F_SET_AC;
if (argc - optind < 1) {
fprintf(stderr, "Usage: bgt %s [options] <bgt-prefix> [...]", argv[0]);
fputc('\n', stderr);
fprintf(stderr, "Options:\n");
fprintf(stderr, " Sample selection:\n");
fprintf(stderr, " -s EXPR samples list (,sample1,sample2 or a file or expr; see Notes below) [all]\n");
fprintf(stderr, " Site selection:\n");
fprintf(stderr, " -r STR region [all]\n");
fprintf(stderr, " -B FILE extract variants overlapping BED FILE []\n");
fprintf(stderr, " -e exclude variants overlapping BED FILE (effective with -B)\n");
fprintf(stderr, " -i INT process from the INT-th record (1-based) []\n");
fprintf(stderr, " -n INT process at most INT records []\n");
fprintf(stderr, " -d FILE variant annotations in FMF (to work with -a) []\n");
fprintf(stderr, " -M load variant annotations in RAM (only with -d)\n");
fprintf(stderr, " -a EXPR alleles list chr:1basedPos:refLen:seq (,allele1,allele2 or a file or expr) []\n");
fprintf(stderr, " -f STR frequency filters []\n");
fprintf(stderr, " VCF output:\n");
fprintf(stderr, " -b BCF output (effective without -S/-H)\n");
fprintf(stderr, " -l INT compression level for BCF [default]\n");
fprintf(stderr, " -u equivalent to -bl0 (overriding -b and -l)\n");
fprintf(stderr, " -G don't output sample genotypes\n");
fprintf(stderr, " -C write AC/AN to the INFO field (auto applied with -f or multipl -s)\n");
fprintf(stderr, " Non-VCF output:\n");
fprintf(stderr, " -S show samples with a set of alleles (with -a)\n");
fprintf(stderr, " -H count of haplotypes with a set of alleles (with -a)\n");
fprintf(stderr, " -t STR comma-delimited list of fields to output. Accepted variables:\n");
fprintf(stderr, " AC, AN, AC#, AN#, CHROM, POS, END, REF, ALT (# for a group number)\n");
fprintf(stderr, "Notes:\n");
fprintf(stderr, " For option -s/-a, EXPR can be one of:\n");
fprintf(stderr, " 1) comma-delimited list following a colon/comma. e.g. -s,NA12878,NA12044\n");
fprintf(stderr, " 2) space-delimited file with the first column giving a sample/allele name. e.g. -s list.txt\n");
fprintf(stderr, " 3) expression if .spl/-d file contains metadata. e.g.: -s\"gender=='M'&&population!='CEU'\"\n");
fprintf(stderr, " If multiple -s is specified, the AC/AN of the first group will be written to VCF INFO AC1/AN1,\n");
fprintf(stderr, " the second to AC2/AN2, etc.\n");
return 1;
}
if (dbfn && in_mem) vardb = fmf_read(dbfn), dbfn = 0;
if ((multi_flag&(BGT_F_CNT_AL|BGT_F_CNT_HAP)) && aexpr == 0) {
fprintf(stderr, "[E::%s] -a must be specified when -S/-H is in use.\n", __func__);
return 1;
}
n_files = argc - optind;
files = (bgt_file_t**)calloc(n_files, sizeof(bgt_file_t*));
for (i = 0; i < n_files; ++i) {
files[i] = bgt_open(argv[optind+i]);
if (files[i] == 0) {
fprintf(stderr, "[E::%s] failed to open BGT with prefix '%s'\n", __func__, argv[optind+i]);
return 1; // FIXME: memory leak
}
}
bm = bgtm_reader_init(n_files, files);
bgtm_set_flag(bm, multi_flag);
if (site_flt && bgtm_set_flt_site(bm, site_flt) != 0) {
fprintf(stderr, "[E::%s] failed to set frequency filters. Syntax error?\n", __func__);
return 1;
}
if (reg && bgtm_set_region(bm, reg) < 0) {
fprintf(stderr, "[E::%s] failed to set region. Region format error?\n", __func__);
return 1;
}
if (bed) bgtm_set_bed(bm, bed, excl);
if (fmt && bgtm_set_table(bm, fmt) < 0) {
fprintf(stderr, "[E::%s] failed to set tabular output.\n", __func__);
return 1;
}
if (seekn > 0) bgtm_set_start(bm, seekn);
if (aexpr) {
int n_al;
n_al = bgtm_set_alleles(bm, aexpr, vardb, dbfn);
if (n_al < 0) {
fprintf(stderr, "[E::%s] failed to set alleles.\n", __func__);
return 1;
} else if (n_al == 0)
fprintf(stderr, "[W::%s] no alleles selected.\n", __func__);
}
for (i = 0; i < n_groups; ++i) {
if (bgtm_add_group(bm, gexpr[i]) < 0) {
fprintf(stderr, "[E::%s] failed to add sample group '%s'.\n", __func__, gexpr[i]);
return 1;
}
}
bgtm_prepare(bm); // bgtm_prepare() generates the VCF header
if (!not_vcf) {
strcpy(modew, "w");
if (out_bcf) strcat(modew, "b");
sprintf(modew + strlen(modew), "%d", clevel);
out = hts_open("-", modew, 0);
vcf_hdr_write(out, bm->h_out);
}
b = bcf_init1();
while (bgtm_read(bm, b) >= 0 && n_read < n_rec) {
if (out) vcf_write1(out, bm->h_out, b);
if (fmt && bm->n_fields > 0) puts(bm->tbl_line.s);
++n_read;
}
bcf_destroy1(b);
if (not_vcf && bm->n_aal > 0) {
if (bm->flag & BGT_F_CNT_HAP) {
bgt_hapcnt_t *hc;
int n_hap;
char *s;
hc = bgtm_hapcnt(bm, &n_hap);
s = bgtm_hapcnt_print_destroy(bm, n_hap, hc);
fputs(s, stdout);
free(s);
}
if (bm->flag & BGT_F_CNT_AL) {
char *s;
if ((s = bgtm_alcnt_print(bm)) != 0)
fputs(s, stdout);
free(s);
}
}
if (out) hts_close(out);
bgtm_reader_destroy(bm);
if (bed) bed_destroy(bed);
for (i = 0; i < n_files; ++i) bgt_close(files[i]);
free(files);
if (vardb) fmf_destroy(vardb);
return 0;
}