void TileManager::reset(BufferParams& params_, int num_samples_)
{
params = params_;
set_samples(num_samples_);
state.buffer = BufferParams();
state.sample = range_start_sample - 1;
state.num_tiles = 0;
state.num_samples = 0;
state.resolution_divider = get_divider(params.width, params.height, start_resolution);
state.render_tiles.clear();
state.denoising_tiles.clear();
state.tiles.clear();
}
static void reheader_vcf(args_t *args)
{
kstring_t hdr = {0,0,0};
htsFile *fp = hts_open(args->fname, "r"); if ( !fp ) error("Failed to open: %s\n", args->fname);
while ( hts_getline(fp, KS_SEP_LINE, &fp->line) >=0 )
{
kputc('\n',&fp->line); // hts_getline eats the newline character
if ( fp->line.s[0]!='#' ) break;
kputsn(fp->line.s,fp->line.l,&hdr);
}
int nsamples = 0;
char **samples = NULL;
if ( args->samples_fname )
samples = hts_readlines(args->samples_fname, &nsamples);
if ( args->header_fname )
{
free(hdr.s); hdr.s = NULL; hdr.l = hdr.m = 0;
read_header_file(args->header_fname, &hdr);
}
if ( samples )
{
set_samples(samples, nsamples, &hdr);
int i;
for (i=0; i<nsamples; i++) free(samples[i]);
free(samples);
}
int out = STDOUT_FILENO;
if ( write(out, hdr.s, hdr.l)!=hdr.l ) error("Failed to write %d bytes\n", hdr.l);
free(hdr.s);
if ( fp->line.l )
{
if ( write(out, fp->line.s, fp->line.l)!=fp->line.l ) error("Failed to write %d bytes\n", fp->line.l);
}
while ( hts_getline(fp, KS_SEP_LINE, &fp->line) >=0 ) // uncompressed file implies small size, we don't worry about speed
{
kputc('\n',&fp->line);
if ( write(out, fp->line.s, fp->line.l)!=fp->line.l ) error("Failed to write %d bytes\n", fp->line.l);
}
hts_close(fp);
}
void Misc::quality_changed(int idx) {
assert((unsigned int)(idx) < Count);
emit set_blocks(Blocks[idx]);
emit set_samples(Samples[idx]);
}
static void reheader_bcf(args_t *args, int is_compressed)
{
htsFile *fp = hts_open(args->fname, "r"); if ( !fp ) error("Failed to open: %s\n", args->fname);
bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to read the header: %s\n", args->fname);
kstring_t htxt = {0,0,0};
int hlen;
htxt.s = bcf_hdr_fmt_text(hdr, 1, &hlen);
htxt.l = hlen;
int i, nsamples = 0;
char **samples = NULL;
if ( args->samples_fname )
samples = hts_readlines(args->samples_fname, &nsamples);
if ( args->header_fname )
{
free(htxt.s); htxt.s = NULL; htxt.l = htxt.m = 0;
read_header_file(args->header_fname, &htxt);
}
if ( samples )
{
set_samples(samples, nsamples, &htxt);
for (i=0; i<nsamples; i++) free(samples[i]);
free(samples);
}
bcf_hdr_t *hdr_out = bcf_hdr_init("r");
bcf_hdr_parse(hdr_out, htxt.s);
if ( args->header_fname ) hdr_out = strip_header(hdr, hdr_out);
// write the header and the body
htsFile *fp_out = hts_open("-",is_compressed ? "wb" : "wbu");
bcf_hdr_write(fp_out, hdr_out);
bcf1_t *rec = bcf_init();
while ( bcf_read(fp, hdr, rec)==0 )
{
// sanity checking, this slows things down. Make it optional?
bcf_unpack(rec, BCF_UN_ALL);
if ( rec->rid >= hdr_out->n[BCF_DT_CTG] || strcmp(bcf_hdr_int2id(hdr,BCF_DT_CTG,rec->rid),bcf_hdr_int2id(hdr_out,BCF_DT_CTG,rec->rid)) )
error("The CHROM is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_CTG,rec->rid));
for (i=0; i<rec->d.n_flt; i++)
{
int id = rec->d.flt[i];
if ( id >= hdr_out->n[BCF_DT_ID] ) break;
if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FLT,id) ) break;
if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) )
error("FIXME: Broken FILTER ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key);
}
if ( i!=rec->d.n_flt )
error("The FILTER is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.flt[i]));
for (i=0; i<rec->n_info; i++)
{
int id = rec->d.info[i].key;
if ( id >= hdr_out->n[BCF_DT_ID] ) break;
if ( !hdr_out->id[BCF_DT_ID][id].key ) break;
if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_INFO,id) ) break;
if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) )
error("FIXME: Broken INFO ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key);
}
if ( i!=rec->n_info )
error("The INFO tag is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.info[i].key));
for (i=0; i<rec->n_fmt; i++)
{
int id = rec->d.fmt[i].id;
if ( id >= hdr_out->n[BCF_DT_ID] ) break;
if ( !hdr_out->id[BCF_DT_ID][id].key ) break;
if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FMT,id) ) break;
if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) )
error("FIXME: Broken FORMAT ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key);
}
if ( i!=rec->n_fmt )
error("The FORMAT tag is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.fmt[i].id));
bcf_write(fp_out,hdr_out,rec);
}
bcf_destroy(rec);
free(htxt.s);
hts_close(fp_out);
hts_close(fp);
bcf_hdr_destroy(hdr_out);
bcf_hdr_destroy(hdr);
}
static void reheader_vcf_gz(args_t *args)
{
BGZF *fp = bgzf_open(args->fname,"r");
if ( !fp || bgzf_read_block(fp) != 0 || !fp->block_length )
error("Failed to read %s: %s\n", args->fname, strerror(errno));
kstring_t hdr = {0,0,0};
char *buffer = (char*) fp->uncompressed_block;
// Read the header and find the position of the data block
if ( buffer[0]!='#' ) error("Could not parse the header, expected '#', found '%c'\n", buffer[0]);
int skip_until = 1; // end of the header in the current uncompressed block
while (1)
{
if ( buffer[skip_until]=='\n' )
{
skip_until++;
if ( skip_until>=fp->block_length )
{
kputsn(buffer,skip_until,&hdr);
if ( bgzf_read_block(fp) != 0 || !fp->block_length ) error("FIXME: No body in the file: %s\n", args->fname);
skip_until = 0;
}
// The header has finished
if ( buffer[skip_until]!='#' )
{
kputsn(buffer,skip_until,&hdr);
break;
}
}
skip_until++;
if ( skip_until>=fp->block_length )
{
kputsn(buffer,fp->block_length,&hdr);
if (bgzf_read_block(fp) != 0 || !fp->block_length) error("FIXME: No body in the file: %s\n", args->fname);
skip_until = 0;
}
}
int nsamples = 0;
char **samples = NULL;
if ( args->samples_fname )
samples = hts_readlines(args->samples_fname, &nsamples);
if ( args->header_fname )
{
free(hdr.s); hdr.s = NULL; hdr.l = hdr.m = 0;
read_header_file(args->header_fname, &hdr);
}
if ( samples )
{
set_samples(samples, nsamples, &hdr);
int i;
for (i=0; i<nsamples; i++) free(samples[i]);
free(samples);
}
// Output the modified header
BGZF *bgzf_out = bgzf_dopen(fileno(stdout), "w");
bgzf_write(bgzf_out, hdr.s, hdr.l);
free(hdr.s);
// Output all remainig data read with the header block
if ( fp->block_length - skip_until > 0 )
{
if ( bgzf_write(bgzf_out, buffer+skip_until, fp->block_length-skip_until)<0 ) error("Error: %d\n",fp->errcode);
}
if ( bgzf_flush(bgzf_out)<0 ) error("Error: %d\n",bgzf_out->errcode);
// Stream the rest of the file without as it is, without decompressing
ssize_t nread;
int page_size = getpagesize();
char *buf = (char*) valloc(page_size);
while (1)
{
nread = bgzf_raw_read(fp, buf, page_size);
if ( nread<=0 ) break;
int count = bgzf_raw_write(bgzf_out, buf, nread);
if (count != nread) error("Write failed, wrote %d instead of %d bytes.\n", count,(int)nread);
}
if (bgzf_close(bgzf_out) < 0) error("Error: %d\n",bgzf_out->errcode);
if (bgzf_close(fp) < 0) error("Error: %d\n",fp->errcode);
free(buf);
}
static void init_data(args_t *args)
{
args->aux.srs = bcf_sr_init();
// Open files for input and output, initialize structures
if ( args->targets )
{
if ( bcf_sr_set_targets(args->aux.srs, args->targets, args->targets_is_file, args->aux.flag&CALL_CONSTR_ALLELES ? 3 : 0)<0 )
error("Failed to read the targets: %s\n", args->targets);
if ( args->aux.flag&CALL_CONSTR_ALLELES && args->flag&CF_INS_MISSED )
{
args->aux.srs->targets->missed_reg_handler = print_missed_line;
args->aux.srs->targets->missed_reg_data = args;
}
}
if ( args->regions )
{
if ( bcf_sr_set_regions(args->aux.srs, args->regions, args->regions_is_file)<0 )
error("Failed to read the targets: %s\n", args->regions);
}
if ( !bcf_sr_add_reader(args->aux.srs, args->bcf_fname) ) error("Failed to open %s: %s\n", args->bcf_fname,bcf_sr_strerror(args->aux.srs->errnum));
args->aux.hdr = bcf_sr_get_header(args->aux.srs,0);
int i;
if ( args->samples_fname )
{
set_samples(args, args->samples_fname, args->samples_is_file);
if ( args->aux.flag&CALL_CONSTR_TRIO )
{
if ( 3*args->aux.nfams!=args->nsamples ) error("Expected only trios in %s, sorry!\n", args->samples_fname);
fprintf(stderr,"Detected %d samples in %d trio families\n", args->nsamples,args->aux.nfams);
}
args->nsex = ploidy_nsex(args->ploidy);
args->sex2ploidy = (int*) calloc(args->nsex,sizeof(int));
args->sex2ploidy_prev = (int*) calloc(args->nsex,sizeof(int));
args->aux.ploidy = (uint8_t*) malloc(args->nsamples);
for (i=0; i<args->nsamples; i++) args->aux.ploidy[i] = 2;
for (i=0; i<args->nsex; i++) args->sex2ploidy_prev[i] = 2;
}
if ( args->samples_map )
{
args->aux.hdr = bcf_hdr_subset(bcf_sr_get_header(args->aux.srs,0), args->nsamples, args->samples, args->samples_map);
if ( !args->aux.hdr ) error("Error occurred while subsetting samples\n");
for (i=0; i<args->nsamples; i++)
if ( args->samples_map[i]<0 ) error("No such sample: %s\n", args->samples[i]);
if ( !bcf_hdr_nsamples(args->aux.hdr) ) error("No matching sample found\n");
}
else
{
args->aux.hdr = bcf_hdr_dup(bcf_sr_get_header(args->aux.srs,0));
for (i=0; i<args->nsamples; i++)
if ( bcf_hdr_id2int(args->aux.hdr,BCF_DT_SAMPLE,args->samples[i])<0 )
error("No such sample: %s\n", args->samples[i]);
}
args->out_fh = hts_open(args->output_fname, hts_bcf_wmode(args->output_type));
if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
if ( args->flag & CF_QCALL )
return;
if ( args->flag & CF_MCALL )
mcall_init(&args->aux);
if ( args->flag & CF_CCALL )
ccall_init(&args->aux);
if ( args->flag&CF_GVCF )
{
bcf_hdr_append(args->aux.hdr,"##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
args->gvcf.rid = -1;
args->gvcf.line = bcf_init1();
args->gvcf.gt = (int32_t*) malloc(2*sizeof(int32_t)*bcf_hdr_nsamples(args->aux.hdr));
for (i=0; i<bcf_hdr_nsamples(args->aux.hdr); i++)
{
args->gvcf.gt[2*i+0] = bcf_gt_unphased(0);
args->gvcf.gt[2*i+1] = bcf_gt_unphased(0);
}
}
bcf_hdr_remove(args->aux.hdr, BCF_HL_INFO, "QS");
bcf_hdr_remove(args->aux.hdr, BCF_HL_INFO, "I16");
bcf_hdr_append_version(args->aux.hdr, args->argc, args->argv, "bcftools_call");
bcf_hdr_write(args->out_fh, args->aux.hdr);
if ( args->flag&CF_INS_MISSED ) init_missed_line(args);
}
