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synced_bcf_reader.c
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synced_bcf_reader.c
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/* synced_bcf_reader.c -- stream through multiple VCF files.
Copyright (C) 2012-2023 Genome Research Ltd.
Author: Petr Danecek <pd3@sanger.ac.uk>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */
#define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h
#include <config.h>
#include <stdlib.h>
#include <assert.h>
#include <stdio.h>
#include <unistd.h>
#include <string.h>
#include <strings.h>
#include <limits.h>
#include <inttypes.h>
#include <errno.h>
#include <sys/stat.h>
#include "htslib/synced_bcf_reader.h"
#include "htslib/kseq.h"
#include "htslib/khash_str2int.h"
#include "htslib/bgzf.h"
#include "htslib/thread_pool.h"
#include "bcf_sr_sort.h"
#define REQUIRE_IDX_ 1
#define ALLOW_NO_IDX_ 2
// Maximum indexable coordinate of .csi, for default min_shift of 14.
// This comes out to about 17 Tbp. Limiting factor is the bin number,
// which is a uint32_t in CSI. The highest number of levels compatible
// with this is 10 (needs 31 bits).
#define MAX_CSI_COOR ((1LL << (14 + 30)) - 1)
typedef struct
{
hts_pos_t start, end; // records are marked for skipping have start>end
}
region1_t;
typedef struct bcf_sr_region_t
{
region1_t *regs; // regions will sorted and merged, redundant records marked for skipping have start>end
int nregs, mregs, creg; // creg: the current active region
}
region_t;
#define BCF_SR_AUX(x) ((aux_t*)((x)->aux))
typedef struct
{
sr_sort_t sort;
int regions_overlap, targets_overlap;
}
aux_t;
static bcf_sr_regions_t *bcf_sr_regions_alloc(void);
static int _regions_add(bcf_sr_regions_t *reg, const char *chr, hts_pos_t start, hts_pos_t end);
static bcf_sr_regions_t *_regions_init_string(const char *str);
static int _regions_match_alleles(bcf_sr_regions_t *reg, int als_idx, bcf1_t *rec);
static void _regions_sort_and_merge(bcf_sr_regions_t *reg);
static int _bcf_sr_regions_overlap(bcf_sr_regions_t *reg, const char *seq, hts_pos_t start, hts_pos_t end, int missed_reg_handler);
static void bcf_sr_seek_start(bcf_srs_t *readers);
char *bcf_sr_strerror(int errnum)
{
switch (errnum)
{
case open_failed:
return strerror(errno);
case not_bgzf:
return "not compressed with bgzip";
case idx_load_failed:
return "could not load index";
case file_type_error:
return "unknown file type";
case api_usage_error:
return "API usage error";
case header_error:
return "could not parse header";
case no_eof:
return "no BGZF EOF marker; file may be truncated";
case no_memory:
return "Out of memory";
case vcf_parse_error:
return "VCF parse error";
case bcf_read_error:
return "BCF read error";
case noidx_error:
return "merge of unindexed files failed";
default: return "";
}
}
int bcf_sr_set_opt(bcf_srs_t *readers, bcf_sr_opt_t opt, ...)
{
va_list args;
switch (opt)
{
case BCF_SR_REQUIRE_IDX:
readers->require_index = REQUIRE_IDX_;
return 0;
case BCF_SR_ALLOW_NO_IDX:
readers->require_index = ALLOW_NO_IDX_;
return 0;
case BCF_SR_PAIR_LOGIC:
va_start(args, opt);
BCF_SR_AUX(readers)->sort.pair = va_arg(args, int);
return 0;
case BCF_SR_REGIONS_OVERLAP:
va_start(args, opt);
BCF_SR_AUX(readers)->regions_overlap = va_arg(args, int);
if ( readers->regions ) readers->regions->overlap = BCF_SR_AUX(readers)->regions_overlap;
return 0;
case BCF_SR_TARGETS_OVERLAP:
va_start(args, opt);
BCF_SR_AUX(readers)->targets_overlap = va_arg(args, int);
if ( readers->targets ) readers->targets->overlap = BCF_SR_AUX(readers)->targets_overlap;
return 0;
default:
break;
}
return 1;
}
static int *init_filters(bcf_hdr_t *hdr, const char *filters, int *nfilters)
{
kstring_t str = {0,0,0};
const char *tmp = filters, *prev = filters;
int nout = 0, *out = NULL;
while ( 1 )
{
if ( *tmp==',' || !*tmp )
{
int *otmp = (int*) realloc(out, (nout+1)*sizeof(int));
if (!otmp)
goto err;
out = otmp;
if ( tmp-prev==1 && *prev=='.' )
{
out[nout] = -1;
nout++;
}
else
{
str.l = 0;
kputsn(prev, tmp-prev, &str);
out[nout] = bcf_hdr_id2int(hdr, BCF_DT_ID, str.s);
if ( out[nout]>=0 ) nout++;
}
if ( !*tmp ) break;
prev = tmp+1;
}
tmp++;
}
if ( str.m ) free(str.s);
*nfilters = nout;
return out;
err:
if (str.m) free(str.s);
free(out);
return NULL;
}
int bcf_sr_set_regions(bcf_srs_t *readers, const char *regions, int is_file)
{
if ( readers->nreaders || readers->regions )
{
if ( readers->regions ) bcf_sr_regions_destroy(readers->regions);
readers->regions = bcf_sr_regions_init(regions,is_file,0,1,-2);
bcf_sr_seek_start(readers);
return 0;
}
readers->regions = bcf_sr_regions_init(regions,is_file,0,1,-2);
if ( !readers->regions ) return -1;
readers->explicit_regs = 1;
readers->require_index = REQUIRE_IDX_;
readers->regions->overlap = BCF_SR_AUX(readers)->regions_overlap;
return 0;
}
int bcf_sr_set_targets(bcf_srs_t *readers, const char *targets, int is_file, int alleles)
{
if ( readers->nreaders || readers->targets )
{
hts_log_error("Must call bcf_sr_set_targets() before bcf_sr_add_reader()");
return -1;
}
if ( targets[0]=='^' )
{
readers->targets_exclude = 1;
targets++;
}
readers->targets = bcf_sr_regions_init(targets,is_file,0,1,-2);
if ( !readers->targets ) return -1;
readers->targets_als = alleles;
readers->targets->overlap = BCF_SR_AUX(readers)->targets_overlap;
return 0;
}
int bcf_sr_set_threads(bcf_srs_t *files, int n_threads)
{
if (!(files->n_threads = n_threads))
return 0;
files->p = calloc(1, sizeof(*files->p));
if (!files->p) {
files->errnum = no_memory;
return -1;
}
if (!(files->p->pool = hts_tpool_init(n_threads)))
return -1;
return 0;
}
void bcf_sr_destroy_threads(bcf_srs_t *files) {
if (!files->p)
return;
if (files->p->pool)
hts_tpool_destroy(files->p->pool);
free(files->p);
}
int bcf_sr_add_reader(bcf_srs_t *files, const char *fname)
{
char fmode[5];
strcpy(fmode, "r");
vcf_open_mode(fmode+1, fname, NULL);
htsFile* file_ptr = hts_open(fname, fmode);
if ( ! file_ptr ) {
files->errnum = open_failed;
return 0;
}
files->has_line = (int*) realloc(files->has_line, sizeof(int)*(files->nreaders+1));
files->has_line[files->nreaders] = 0;
files->readers = (bcf_sr_t*) realloc(files->readers, sizeof(bcf_sr_t)*(files->nreaders+1));
bcf_sr_t *reader = &files->readers[files->nreaders++];
memset(reader,0,sizeof(bcf_sr_t));
reader->file = file_ptr;
files->errnum = 0;
if ( reader->file->format.compression==bgzf )
{
BGZF *bgzf = hts_get_bgzfp(reader->file);
if ( bgzf && bgzf_check_EOF(bgzf) == 0 ) {
files->errnum = no_eof;
hts_log_warning("No BGZF EOF marker; file '%s' may be truncated", fname);
}
if (files->p)
bgzf_thread_pool(bgzf, files->p->pool, files->p->qsize);
}
if ( files->require_index==REQUIRE_IDX_ )
{
if ( reader->file->format.format==vcf )
{
if ( reader->file->format.compression!=bgzf )
{
files->errnum = not_bgzf;
return 0;
}
reader->tbx_idx = tbx_index_load(fname);
if ( !reader->tbx_idx )
{
files->errnum = idx_load_failed;
return 0;
}
reader->header = bcf_hdr_read(reader->file);
}
else if ( reader->file->format.format==bcf )
{
if ( reader->file->format.compression!=bgzf )
{
files->errnum = not_bgzf;
return 0;
}
reader->header = bcf_hdr_read(reader->file);
reader->bcf_idx = bcf_index_load(fname);
if ( !reader->bcf_idx )
{
files->errnum = idx_load_failed;
return 0;
}
}
else
{
files->errnum = file_type_error;
return 0;
}
}
else
{
if ( reader->file->format.format==bcf || reader->file->format.format==vcf )
{
reader->header = bcf_hdr_read(reader->file);
}
else
{
files->errnum = file_type_error;
return 0;
}
files->streaming = 1;
}
if ( files->streaming && files->nreaders>1 )
{
static int no_index_warned = 0;
if ( files->require_index==ALLOW_NO_IDX_ && !no_index_warned )
{
hts_log_warning("Using multiple unindexed files may produce errors, make sure chromosomes are in the same order!");
no_index_warned = 1;
}
if ( files->require_index!=ALLOW_NO_IDX_ )
{
files->errnum = api_usage_error;
hts_log_error("Must set require_index when the number of readers is greater than one");
return 0;
}
}
if ( files->streaming && files->regions )
{
files->errnum = api_usage_error;
hts_log_error("Cannot tabix-jump in streaming mode");
return 0;
}
if ( !reader->header )
{
files->errnum = header_error;
return 0;
}
reader->fname = strdup(fname);
if ( files->apply_filters )
reader->filter_ids = init_filters(reader->header, files->apply_filters, &reader->nfilter_ids);
// Update list of chromosomes
if ( !files->explicit_regs && !files->streaming )
{
int n = 0, i;
const char **names;
if ( !files->regions )
{
files->regions = bcf_sr_regions_alloc();
if ( !files->regions )
{
hts_log_error("Cannot allocate regions data structure");
return 0;
}
}
names = reader->tbx_idx ? tbx_seqnames(reader->tbx_idx, &n) : bcf_hdr_seqnames(reader->header, &n);
for (i=0; i<n; i++)
{
_regions_add(files->regions, names[i], -1, -1);
}
free(names);
_regions_sort_and_merge(files->regions);
}
if ( files->require_index==ALLOW_NO_IDX_ && files->nreaders > 1 )
{
bcf_hdr_t *hdr0 = files->readers[0].header;
bcf_hdr_t *hdr1 = reader->header;
if ( hdr0->n[BCF_DT_CTG]!=hdr1->n[BCF_DT_CTG] )
{
files->errnum = noidx_error;
hts_log_error("Different number of sequences in the header, refusing to stream multiple unindexed files");
return 0;
}
int i;
for (i=0; i<hdr0->n[BCF_DT_CTG]; i++)
{
if ( strcmp(bcf_hdr_id2name(hdr0,i),bcf_hdr_id2name(hdr1,i)) )
{
files->errnum = noidx_error;
hts_log_error("Sequences in the header appear in different order, refusing to stream multiple unindexed files");
return 0;
}
}
}
return 1;
}
bcf_srs_t *bcf_sr_init(void)
{
bcf_srs_t *files = (bcf_srs_t*) calloc(1,sizeof(bcf_srs_t));
files->aux = (aux_t*) calloc(1,sizeof(aux_t));
bcf_sr_sort_init(&BCF_SR_AUX(files)->sort);
bcf_sr_set_opt(files,BCF_SR_REGIONS_OVERLAP,1);
bcf_sr_set_opt(files,BCF_SR_TARGETS_OVERLAP,0);
return files;
}
static void bcf_sr_destroy1(bcf_sr_t *reader)
{
free(reader->fname);
if ( reader->tbx_idx ) tbx_destroy(reader->tbx_idx);
if ( reader->bcf_idx ) hts_idx_destroy(reader->bcf_idx);
bcf_hdr_destroy(reader->header);
hts_close(reader->file);
if ( reader->itr ) tbx_itr_destroy(reader->itr);
int j;
for (j=0; j<reader->mbuffer; j++)
bcf_destroy1(reader->buffer[j]);
free(reader->buffer);
free(reader->samples);
free(reader->filter_ids);
}
void bcf_sr_destroy(bcf_srs_t *files)
{
int i;
for (i=0; i<files->nreaders; i++)
bcf_sr_destroy1(&files->readers[i]);
free(files->has_line);
free(files->readers);
for (i=0; i<files->n_smpl; i++) free(files->samples[i]);
free(files->samples);
if (files->targets) bcf_sr_regions_destroy(files->targets);
if (files->regions) bcf_sr_regions_destroy(files->regions);
if (files->tmps.m) free(files->tmps.s);
if (files->n_threads) bcf_sr_destroy_threads(files);
bcf_sr_sort_destroy(&BCF_SR_AUX(files)->sort);
free(files->aux);
free(files);
}
void bcf_sr_remove_reader(bcf_srs_t *files, int i)
{
assert( !files->samples ); // not ready for this yet
bcf_sr_sort_remove_reader(files, &BCF_SR_AUX(files)->sort, i);
bcf_sr_destroy1(&files->readers[i]);
if ( i+1 < files->nreaders )
{
memmove(&files->readers[i], &files->readers[i+1], (files->nreaders-i-1)*sizeof(bcf_sr_t));
memmove(&files->has_line[i], &files->has_line[i+1], (files->nreaders-i-1)*sizeof(int));
}
files->nreaders--;
}
#if DEBUG_SYNCED_READER
void debug_buffer(FILE *fp, bcf_sr_t *reader)
{
int j;
for (j=0; j<=reader->nbuffer; j++)
{
bcf1_t *line = reader->buffer[j];
fprintf(fp,"\t%p\t%s%s\t%s:%"PRIhts_pos"\t%s ", (void*)line,reader->fname,j==0?"*":" ",reader->header->id[BCF_DT_CTG][line->rid].key,line->pos+1,line->n_allele?line->d.allele[0]:"");
int k;
for (k=1; k<line->n_allele; k++) fprintf(fp," %s", line->d.allele[k]);
fprintf(fp,"\n");
}
}
void debug_buffers(FILE *fp, bcf_srs_t *files)
{
int i;
for (i=0; i<files->nreaders; i++)
{
fprintf(fp, "has_line: %d\t%s\n", bcf_sr_has_line(files,i),files->readers[i].fname);
debug_buffer(fp, &files->readers[i]);
}
fprintf(fp,"\n");
}
#endif
static inline int has_filter(bcf_sr_t *reader, bcf1_t *line)
{
int i, j;
if ( !line->d.n_flt )
{
for (j=0; j<reader->nfilter_ids; j++)
if ( reader->filter_ids[j]<0 ) return 1;
return 0;
}
for (i=0; i<line->d.n_flt; i++)
{
for (j=0; j<reader->nfilter_ids; j++)
if ( line->d.flt[i]==reader->filter_ids[j] ) return 1;
}
return 0;
}
static int _reader_seek(bcf_sr_t *reader, const char *seq, hts_pos_t start, hts_pos_t end)
{
if ( end>=MAX_CSI_COOR )
{
hts_log_error("The coordinate is out of csi index limit: %"PRIhts_pos, end+1);
exit(1);
}
if ( reader->itr )
{
hts_itr_destroy(reader->itr);
reader->itr = NULL;
}
reader->nbuffer = 0;
if ( reader->tbx_idx )
{
int tid = tbx_name2id(reader->tbx_idx, seq);
if ( tid==-1 ) return -1; // the sequence not present in this file
reader->itr = tbx_itr_queryi(reader->tbx_idx,tid,start,end+1);
}
else
{
int tid = bcf_hdr_name2id(reader->header, seq);
if ( tid==-1 ) return -1; // the sequence not present in this file
reader->itr = bcf_itr_queryi(reader->bcf_idx,tid,start,end+1);
}
if (!reader->itr) {
hts_log_error("Could not seek: %s:%"PRIhts_pos"-%"PRIhts_pos, seq, start + 1, end + 1);
abort();
}
return 0;
}
/*
* _readers_next_region() - jumps to next region if necessary
* Returns 0 on success or -1 when there are no more regions left
*/
static int _readers_next_region(bcf_srs_t *files)
{
// Need to open new chromosome? Check number of lines in all readers' buffers
int i, eos = 0;
for (i=0; i<files->nreaders; i++)
if ( !files->readers[i].itr && !files->readers[i].nbuffer ) eos++;
if ( eos!=files->nreaders )
{
// Some of the readers still has buffered lines
return 0;
}
// No lines in the buffer, need to open new region or quit.
int prev_iseq = files->regions->iseq;
hts_pos_t prev_end = files->regions->end;
if ( bcf_sr_regions_next(files->regions)<0 ) return -1;
files->regions->prev_end = prev_iseq==files->regions->iseq ? prev_end : -1;
for (i=0; i<files->nreaders; i++)
_reader_seek(&files->readers[i],files->regions->seq_names[files->regions->iseq],files->regions->start,files->regions->end);
return 0;
}
static void _set_variant_boundaries(bcf1_t *rec, hts_pos_t *beg, hts_pos_t *end)
{
hts_pos_t off;
if ( rec->n_allele )
{
off = rec->rlen;
bcf_unpack(rec, BCF_UN_STR);
int i;
for (i=1; i<rec->n_allele; i++)
{
// Make symbolic alleles start at POS, although this is not strictly true for
// <DEL>,<INS> where POS should be the position BEFORE the deletion/insertion.
// However, since arbitrary symbolic alleles can be defined by the user, we
// will simplify the interpretation of --targets-overlap and --region-overlap.
int j = 0;
char *ref = rec->d.allele[0];
char *alt = rec->d.allele[i];
while ( ref[j] && alt[j] && ref[j]==alt[j] ) j++;
if ( off > j ) off = j;
if ( !off ) break;
}
}
else
off = 0;
*beg = rec->pos + off;
*end = rec->pos + rec->rlen - 1;
}
/*
* _reader_fill_buffer() - buffers all records with the same coordinate
*/
static int _reader_fill_buffer(bcf_srs_t *files, bcf_sr_t *reader)
{
// Return if the buffer is full: the coordinate of the last buffered record differs
if ( reader->nbuffer && reader->buffer[reader->nbuffer]->pos != reader->buffer[1]->pos ) return 0;
// No iterator (sequence not present in this file) and not streaming
if ( !reader->itr && !files->streaming ) return 0;
// Fill the buffer with records starting at the same position
int i, ret = 0;
while (1)
{
if ( reader->nbuffer+1 >= reader->mbuffer )
{
// Increase buffer size
reader->mbuffer += 8;
reader->buffer = (bcf1_t**) realloc(reader->buffer, sizeof(bcf1_t*)*reader->mbuffer);
for (i=8; i>0; i--) // initialize
{
reader->buffer[reader->mbuffer-i] = bcf_init1();
reader->buffer[reader->mbuffer-i]->max_unpack = files->max_unpack;
reader->buffer[reader->mbuffer-i]->pos = -1; // for rare cases when VCF starts from 1
}
}
if ( files->streaming )
{
if ( reader->file->format.format==vcf )
{
ret = hts_getline(reader->file, KS_SEP_LINE, &files->tmps);
if ( ret < -1 ) files->errnum = bcf_read_error;
if ( ret < 0 ) break; // no more lines or an error
ret = vcf_parse1(&files->tmps, reader->header, reader->buffer[reader->nbuffer+1]);
if ( ret<0 ) { files->errnum = vcf_parse_error; break; }
}
else if ( reader->file->format.format==bcf )
{
ret = bcf_read1(reader->file, reader->header, reader->buffer[reader->nbuffer+1]);
if ( ret < -1 ) files->errnum = bcf_read_error;
if ( ret < 0 ) break; // no more lines or an error
}
else
{
hts_log_error("Fixme: not ready for this");
exit(1);
}
}
else if ( reader->tbx_idx )
{
ret = tbx_itr_next(reader->file, reader->tbx_idx, reader->itr, &files->tmps);
if ( ret < -1 ) files->errnum = bcf_read_error;
if ( ret < 0 ) break; // no more lines or an error
ret = vcf_parse1(&files->tmps, reader->header, reader->buffer[reader->nbuffer+1]);
if ( ret<0 ) { files->errnum = vcf_parse_error; break; }
}
else
{
ret = bcf_itr_next(reader->file, reader->itr, reader->buffer[reader->nbuffer+1]);
if ( ret < -1 ) files->errnum = bcf_read_error;
if ( ret < 0 ) break; // no more lines or an error
bcf_subset_format(reader->header,reader->buffer[reader->nbuffer+1]);
}
// Prevent creation of duplicates from records overlapping multiple regions
// and recognize true variant overlaps vs record overlaps (e.g. TA>T vs A>-)
if ( files->regions )
{
hts_pos_t beg, end;
if ( BCF_SR_AUX(files)->regions_overlap==0 )
beg = end = reader->buffer[reader->nbuffer+1]->pos;
else if ( BCF_SR_AUX(files)->regions_overlap==1 )
{
beg = reader->buffer[reader->nbuffer+1]->pos;
end = reader->buffer[reader->nbuffer+1]->pos + reader->buffer[reader->nbuffer+1]->rlen - 1;
}
else if ( BCF_SR_AUX(files)->regions_overlap==2 )
_set_variant_boundaries(reader->buffer[reader->nbuffer+1], &beg,&end);
else
{
hts_log_error("This should never happen, just to keep clang compiler happy: %d",BCF_SR_AUX(files)->targets_overlap);
exit(1);
}
if ( beg <= files->regions->prev_end || end < files->regions->start || beg > files->regions->end ) continue;
}
// apply filter
if ( !reader->nfilter_ids )
bcf_unpack(reader->buffer[reader->nbuffer+1], BCF_UN_STR);
else
{
bcf_unpack(reader->buffer[reader->nbuffer+1], BCF_UN_STR|BCF_UN_FLT);
if ( !has_filter(reader, reader->buffer[reader->nbuffer+1]) ) continue;
}
reader->nbuffer++;
if ( reader->buffer[reader->nbuffer]->rid != reader->buffer[1]->rid ) break;
if ( reader->buffer[reader->nbuffer]->pos != reader->buffer[1]->pos ) break; // the buffer is full
}
if ( ret<0 )
{
// done for this region
tbx_itr_destroy(reader->itr);
reader->itr = NULL;
}
if ( files->require_index==ALLOW_NO_IDX_ && reader->buffer[reader->nbuffer]->rid < reader->buffer[1]->rid )
{
hts_log_error("Sequences out of order, cannot stream multiple unindexed files: %s", reader->fname);
exit(1);
}
return 0; // FIXME: Check for more errs in this function
}
/*
* _readers_shift_buffer() - removes the first line
*/
static void _reader_shift_buffer(bcf_sr_t *reader)
{
if ( !reader->nbuffer ) return;
int i;
bcf1_t *tmp = reader->buffer[1];
for (i=2; i<=reader->nbuffer; i++)
reader->buffer[i-1] = reader->buffer[i];
if ( reader->nbuffer > 1 )
reader->buffer[reader->nbuffer] = tmp;
reader->nbuffer--;
}
static int next_line(bcf_srs_t *files)
{
const char *chr = NULL;
hts_pos_t min_pos = HTS_POS_MAX;
// Loop until next suitable line is found or all readers have finished
while ( 1 )
{
// Get all readers ready for the next region.
if ( files->regions && _readers_next_region(files)<0 ) break;
// Fill buffers and find the minimum chromosome
int i, min_rid = INT32_MAX;
for (i=0; i<files->nreaders; i++)
{
_reader_fill_buffer(files, &files->readers[i]);
if ( files->require_index==ALLOW_NO_IDX_ )
{
if ( !files->readers[i].nbuffer ) continue;
if ( min_rid > files->readers[i].buffer[1]->rid ) min_rid = files->readers[i].buffer[1]->rid;
}
}
for (i=0; i<files->nreaders; i++)
{
if ( !files->readers[i].nbuffer ) continue;
if ( files->require_index==ALLOW_NO_IDX_ && min_rid != files->readers[i].buffer[1]->rid ) continue;
// Update the minimum coordinate
if ( min_pos > files->readers[i].buffer[1]->pos )
{
min_pos = files->readers[i].buffer[1]->pos;
chr = bcf_seqname(files->readers[i].header, files->readers[i].buffer[1]);
assert(chr);
bcf_sr_sort_set_active(&BCF_SR_AUX(files)->sort, i);
}
else if ( min_pos==files->readers[i].buffer[1]->pos )
bcf_sr_sort_add_active(&BCF_SR_AUX(files)->sort, i);
}
if ( min_pos==HTS_POS_MAX )
{
if ( !files->regions ) break;
continue;
}
// Skip this position if not present in targets
if ( files->targets )
{
int match = 0;
for (i=0; i<files->nreaders; i++)
{
if ( !files->readers[i].nbuffer || files->readers[i].buffer[1]->pos!=min_pos ) continue;
hts_pos_t beg, end;
if ( BCF_SR_AUX(files)->targets_overlap==0 )
beg = end = min_pos;
else if ( BCF_SR_AUX(files)->targets_overlap==1 )
{
beg = min_pos;
end = min_pos + files->readers[i].buffer[1]->rlen - 1;
}
else if ( BCF_SR_AUX(files)->targets_overlap==2 )
_set_variant_boundaries(files->readers[i].buffer[1], &beg,&end);
else
{
hts_log_error("This should never happen, just to keep clang compiler happy: %d",BCF_SR_AUX(files)->targets_overlap);
exit(1);
}
int overlap = bcf_sr_regions_overlap(files->targets, chr, beg, end)==0 ? 1 : 0;
if ( (!files->targets_exclude && !overlap) || (files->targets_exclude && overlap) )
_reader_shift_buffer(&files->readers[i]);
else
match = 1;
}
if ( !match )
{
min_pos = HTS_POS_MAX;
chr = NULL;
continue;
}
}
break; // done: chr and min_pos are set
}
if ( !chr ) return 0;
return bcf_sr_sort_next(files, &BCF_SR_AUX(files)->sort, chr, min_pos);
}
int bcf_sr_next_line(bcf_srs_t *files)
{
if ( !files->targets_als )
return next_line(files);
while (1)
{
int i, ret = next_line(files);
if ( !ret ) return ret;
for (i=0; i<files->nreaders; i++)
if ( files->has_line[i] ) break;
if ( _regions_match_alleles(files->targets, files->targets_als-1, files->readers[i].buffer[0]) ) return ret;
// Check if there are more duplicate lines in the buffers. If not, return this line as if it
// matched the targets, even if there is a type mismatch
for (i=0; i<files->nreaders; i++)
{
if ( !files->has_line[i] ) continue;
if ( files->readers[i].nbuffer==0 || files->readers[i].buffer[1]->pos!=files->readers[i].buffer[0]->pos ) continue;
break;
}
if ( i==files->nreaders ) return ret; // no more lines left, output even if target alleles are not of the same type
}
}
static void bcf_sr_seek_start(bcf_srs_t *readers)
{
bcf_sr_regions_t *reg = readers->regions;
int i;
for (i=0; i<reg->nseqs; i++)
reg->regs[i].creg = -1;
reg->iseq = 0;
reg->start = -1;
reg->end = -1;
reg->prev_seq = -1;
reg->prev_start = -1;
reg->prev_end = -1;
}
int bcf_sr_seek(bcf_srs_t *readers, const char *seq, hts_pos_t pos)
{
if ( !readers->regions ) return 0;
bcf_sr_sort_reset(&BCF_SR_AUX(readers)->sort);
if ( !seq && !pos )
{
// seek to start
bcf_sr_seek_start(readers);
return 0;
}
int i, nret = 0;
// Need to position both the readers and the regions. The latter is a bit of a mess
// because we can have in memory or external regions. The safe way is:
// - reset all regions as if they were not read from at all (bcf_sr_seek_start)
// - find the requested iseq (stored in the seq_hash)
// - position regions to the requested position (bcf_sr_regions_overlap)
bcf_sr_seek_start(readers);
if ( khash_str2int_get(readers->regions->seq_hash, seq, &i)>=0 ) readers->regions->iseq = i;
_bcf_sr_regions_overlap(readers->regions, seq, pos, pos, 0);
for (i=0; i<readers->nreaders; i++)
{
nret += _reader_seek(&readers->readers[i],seq,pos,MAX_CSI_COOR-1);
}
return nret;
}
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 )
{
hts_log_error("Could not read the file: \"%s\"", 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 )
{
hts_log_warning("The sample \"%s\" was not found in %s, skipping",
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 )
hts_log_warning("No samples in common");
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;
}
// Allocate a new region list structure.
static bcf_sr_regions_t *bcf_sr_regions_alloc(void)
{
bcf_sr_regions_t *reg = (bcf_sr_regions_t *) calloc(1, sizeof(bcf_sr_regions_t));
if ( !reg ) return NULL;
reg->start = reg->end = -1;
reg->prev_start = reg->prev_end = reg->prev_seq = -1;
return reg;
}
// Add a new region into a list. On input the coordinates are 1-based, inclusive, then stored 0-based,
// inclusive. Sorting and merging step needed afterwards: qsort(..,cmp_regions) and merge_regions().
static int _regions_add(bcf_sr_regions_t *reg, const char *chr, hts_pos_t start, hts_pos_t end)
{
if ( start==-1 && end==-1 )
{
start = 0; end = MAX_CSI_COOR-1;
}
else
{
start--; end--; // store 0-based coordinates
}
if ( !reg->seq_hash )
reg->seq_hash = khash_str2int_init();
int iseq;
if ( khash_str2int_get(reg->seq_hash, chr, &iseq)<0 )
{
// the chromosome block does not exist