void bcf_sr_regions_destroy(bcf_sr_regions_t *reg)
{
int i;
free(reg->fname);
if ( reg->itr ) tbx_itr_destroy(reg->itr);
if ( reg->tbx ) tbx_destroy(reg->tbx);
if ( reg->file ) hts_close(reg->file);
if ( reg->als ) free(reg->als);
if ( reg->als_str.s ) free(reg->als_str.s);
free(reg->line.s);
if ( reg->regs )
{
// free only in-memory names, tbx names are const
for (i=0; i<reg->nseqs; i++)
{
free(reg->seq_names[i]);
free(reg->regs[i].regs);
}
}
free(reg->regs);
free(reg->seq_names);
khash_str2int_destroy(reg->seq_hash);
free(reg);
}
int bcf_sr_set_samples(bcf_srs_t *files, const char *fname, int is_file)
{
int i, j, nsmpl, free_smpl = 0;
char **smpl = NULL;
void *exclude = (fname[0]=='^') ? khash_str2int_init() : NULL;
if ( exclude || strcmp("-",fname) ) // "-" stands for all samples
{
smpl = hts_readlist(fname, is_file, &nsmpl);
if ( !smpl )
{
fprintf(stderr,"Could not read the file: \"%s\"\n", fname);
return 0;
}
if ( exclude )
{
for (i=0; i<nsmpl; i++)
khash_str2int_inc(exclude, smpl[i]);
}
free_smpl = 1;
}
if ( !smpl )
{
smpl = files->readers[0].header->samples; // intersection of all samples
nsmpl = bcf_hdr_nsamples(files->readers[0].header);
}
files->samples = NULL;
files->n_smpl = 0;
for (i=0; i<nsmpl; i++)
{
if ( exclude && khash_str2int_has_key(exclude,smpl[i]) ) continue;
int n_isec = 0;
for (j=0; j<files->nreaders; j++)
{
if ( bcf_hdr_id2int(files->readers[j].header, BCF_DT_SAMPLE, smpl[i])<0 ) break;
n_isec++;
}
if ( n_isec!=files->nreaders )
{
fprintf(stderr,"Warning: The sample \"%s\" was not found in %s, skipping\n", smpl[i], files->readers[n_isec].fname);
continue;
}
files->samples = (char**) realloc(files->samples, (files->n_smpl+1)*sizeof(const char*));
files->samples[files->n_smpl++] = strdup(smpl[i]);
}
if ( exclude ) khash_str2int_destroy(exclude);
if ( free_smpl )
{
for (i=0; i<nsmpl; i++) free(smpl[i]);
free(smpl);
}
if ( !files->n_smpl )
{
if ( files->nreaders>1 )
fprintf(stderr,"No samples in common.\n");
return 0;
}
for (i=0; i<files->nreaders; i++)
{
bcf_sr_t *reader = &files->readers[i];
reader->samples = (int*) malloc(sizeof(int)*files->n_smpl);
reader->n_smpl = files->n_smpl;
for (j=0; j<files->n_smpl; j++)
reader->samples[j] = bcf_hdr_id2int(reader->header, BCF_DT_SAMPLE, files->samples[j]);
}
return 1;
}
static void init_data(args_t *args)
{
int i;
args->hdr = args->files->readers[0].header;
if (args->calc_ac && args->update_info)
{
bcf_hdr_append(args->hdr,"##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes\">");
bcf_hdr_append(args->hdr,"##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">");
}
bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_view");
// setup sample data
if (args->sample_names)
{
void *hdr_samples = khash_str2int_init();
for (i=0; i<bcf_hdr_nsamples(args->hdr); i++)
khash_str2int_inc(hdr_samples, bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i));
void *exclude = (args->sample_names[0]=='^') ? khash_str2int_init() : NULL;
int nsmpl;
char **smpl = NULL;
args->samples = NULL; args->n_samples = 0;
smpl = hts_readlist(exclude ? &args->sample_names[1] : args->sample_names, args->sample_is_file, &nsmpl);
if ( !smpl )
{
error("Could not read the list: \"%s\"\n", exclude ? &args->sample_names[1] : args->sample_names);
}
if ( exclude )
{
for (i=0; i<nsmpl; i++) {
if (!khash_str2int_has_key(hdr_samples,smpl[i])) {
if (args->force_samples) {
fprintf(stderr, "Warn: exclude called for sample that does not exist in header: \"%s\"... skipping\n", smpl[i]);
} else {
error("Error: exclude called for sample that does not exist in header: \"%s\". Use \"--force-samples\" to ignore this error.\n", smpl[i]);
}
}
khash_str2int_inc(exclude, smpl[i]);
}
for (i=0; i<bcf_hdr_nsamples(args->hdr); i++)
{
if ( exclude && khash_str2int_has_key(exclude,bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i)) ) continue;
args->samples = (char**) realloc(args->samples, (args->n_samples+1)*sizeof(const char*));
args->samples[args->n_samples++] = strdup(bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i));
}
khash_str2int_destroy(exclude);
}
else
{
for (i=0; i<nsmpl; i++) {
if (!khash_str2int_has_key(hdr_samples,smpl[i])) {
if (args->force_samples) {
fprintf(stderr, "Warn: subset called for sample that does not exist in header: \"%s\"... skipping\n", smpl[i]);
continue;
} else {
error("Error: subset called for sample that does not exist in header: \"%s\". Use \"--force-samples\" to ignore this error.\n", smpl[i]);
}
}
args->samples = (char**) realloc(args->samples, (args->n_samples+1)*sizeof(const char*));
args->samples[args->n_samples++] = strdup(smpl[i]);
}
}
for (i=0; i<nsmpl; i++) free(smpl[i]);
free(smpl);
khash_str2int_destroy(hdr_samples);
if (args->n_samples == 0) {
fprintf(stderr, "Warn: subsetting has removed all samples\n");
args->sites_only = 1;
}
}
if (args->n_samples)
args->imap = (int*)malloc(args->n_samples * sizeof(int));
// determine variant types to include/exclude
if (args->include_types || args->exclude_types) {
if (args->include_types && args->exclude_types) {
fprintf(stderr, "Error: only supply one of --include-types, --exclude-types options\n");
exit(1);
}
char **type_list = 0;
int m = 0, n = 0;
const char *q, *p;
for (q = p = args->include_types ? args->include_types : args->exclude_types;; ++p) {
if (*p == ',' || *p == 0) {
if (m == n) {
m = m? m<<1 : 16;
type_list = (char**)realloc(type_list, m * sizeof(char*));
}
type_list[n] = (char*)calloc(p - q + 1, 1);
strncpy(type_list[n++], q, p - q);
q = p + 1;
if (*p == 0) break;
}
}
type_list = (char**)realloc(type_list, n * sizeof(char*));
if (args->include_types) {
args->include = 0;
for (i = 0; i < n; ++i) {
if (strcmp(type_list[i], "snps") == 0) args->include |= VCF_SNP;
else if (strcmp(type_list[i], "indels") == 0) args->include |= VCF_INDEL;
else if (strcmp(type_list[i], "mnps") == 0) args->include |= VCF_MNP;
else if (strcmp(type_list[i], "other") == 0) args->include |= VCF_OTHER;
else {
fprintf(stderr, "[E::%s] unknown type\n", type_list[i]);
fprintf(stderr, "Accepted types are snps, indels, mnps, other\n");
exit(1);
}
}
}
if (args->exclude_types) {
args->exclude = 0;
for (i = 0; i < n; ++i) {
if (strcmp(type_list[i], "snps") == 0) args->exclude |= VCF_SNP;
else if (strcmp(type_list[i], "indels") == 0) args->exclude |= VCF_INDEL;
else if (strcmp(type_list[i], "mnps") == 0) args->exclude |= VCF_MNP;
else if (strcmp(type_list[i], "other") == 0) args->exclude |= VCF_OTHER;
else {
fprintf(stderr, "[E::%s] unknown type\n", type_list[i]);
fprintf(stderr, "Accepted types are snps, indels, mnps, other\n");
exit(1);
}
}
}
for (i = 0; i < n; ++i)
free(type_list[i]);
free(type_list);
}
// setup output
char modew[8];
strcpy(modew, "w");
if (args->clevel >= 0 && args->clevel <= 9) sprintf(modew + 1, "%d", args->clevel);
if (args->output_type==FT_BCF) strcat(modew, "bu"); // uncompressed BCF
else if (args->output_type & FT_BCF) strcat(modew, "b"); // compressed BCF
else if (args->output_type & FT_GZ) strcat(modew,"z"); // compressed VCF
args->out = hts_open(args->fn_out ? args->fn_out : "-", modew);
if ( !args->out ) error("%s: %s\n", args->fn_out,strerror(errno));
// headers: hdr=full header, hsub=subset header, hnull=sites only header
if (args->sites_only){
args->hnull = bcf_hdr_subset(args->hdr, 0, 0, 0);
bcf_hdr_remove(args->hnull, BCF_HL_FMT, NULL);
}
if (args->n_samples > 0)
{
args->hsub = bcf_hdr_subset(args->hdr, args->n_samples, args->samples, args->imap);
if ( !args->hsub ) error("Error occurred while subsetting samples\n");
if ( args->n_samples != bcf_hdr_nsamples(args->hsub) )
{
int i;
for (i=0; i<args->n_samples; i++)
if ( args->imap[i]<0 ) error("Error: No such sample: \"%s\"\n", args->samples[i]);
}
}
if ( args->filter_str )
args->filter = filter_init(args->hdr, args->filter_str);
}
