Mercurial > repos > youngkim > ezbamqc
diff ezBAMQC/src/htslib/synced_bcf_reader.c @ 0:dfa3745e5fd8
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| author | youngkim |
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| date | Thu, 24 Mar 2016 17:12:52 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ezBAMQC/src/htslib/synced_bcf_reader.c Thu Mar 24 17:12:52 2016 -0400 @@ -0,0 +1,1257 @@ +/* synced_bcf_reader.c -- stream through multiple VCF files. + + Copyright (C) 2012-2014 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. */ + +#include <stdio.h> +#include <unistd.h> +#include <string.h> +#include <limits.h> +#include <errno.h> +#include <ctype.h> +#include <sys/stat.h> +#include "htslib/synced_bcf_reader.h" +#include "htslib/kseq.h" +#include "htslib/khash_str2int.h" + +#define MAX_CSI_COOR 0x7fffffff // maximum indexable coordinate of .csi + +typedef struct +{ + uint32_t start, end; +} +region1_t; + +typedef struct _region_t +{ + region1_t *regs; + int nregs, mregs, creg; +} +region_t; + +static void _regions_add(bcf_sr_regions_t *reg, const char *chr, int start, int 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); + +char *bcf_sr_strerror(int errnum) +{ + switch (errnum) + { + case open_failed: + return strerror(errno); break; + case not_bgzf: + return "not compressed with bgzip"; break; + case idx_load_failed: + return "could not load index"; break; + case file_type_error: + return "unknown file type"; break; + case api_usage_error: + return "API usage error"; break; + case header_error: + return "could not parse header"; break; + default: return ""; + } +} + +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 ) + { + out = (int*) realloc(out, (nout+1)*sizeof(int)); + if ( tmp-prev==1 && *prev=='.' ) + out[nout] = -1; + else + { + str.l = 0; + kputsn(prev, tmp-prev, &str); + out[nout] = bcf_hdr_id2int(hdr, BCF_DT_ID, str.s); + } + nout++; + if ( !*tmp ) break; + prev = tmp+1; + } + tmp++; + } + if ( str.m ) free(str.s); + *nfilters = nout; + return out; +} + +int bcf_sr_set_regions(bcf_srs_t *readers, const char *regions, int is_file) +{ + assert( !readers->regions ); + if ( readers->nreaders ) + { + fprintf(stderr,"[%s:%d %s] Error: bcf_sr_set_regions() must be called before bcf_sr_add_reader()\n", __FILE__,__LINE__,__FUNCTION__); + return -1; + } + readers->regions = bcf_sr_regions_init(regions,is_file,0,1,-2); + if ( !readers->regions ) return -1; + readers->explicit_regs = 1; + readers->require_index = 1; + return 0; +} +int bcf_sr_set_targets(bcf_srs_t *readers, const char *targets, int is_file, int alleles) +{ + assert( !readers->targets ); + 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; + return 0; +} + +int bcf_sr_add_reader(bcf_srs_t *files, const char *fname) +{ + htsFile* file_ptr = hts_open(fname, "r"); + 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 ( files->require_index ) + { + 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 ) + { + files->errnum = api_usage_error; + fprintf(stderr,"[%s:%d %s] Error: %d readers, yet require_index not set\n", __FILE__,__LINE__,__FUNCTION__,files->nreaders); + return 0; + } + if ( files->streaming && files->regions ) + { + files->errnum = api_usage_error; + fprintf(stderr,"[%s:%d %s] Error: cannot tabix-jump in streaming mode\n", __FILE__,__LINE__,__FUNCTION__); + return 0; + } + if ( !reader->header ) + { + files->errnum = header_error; + return 0; + } + + reader->fname = 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,i; + const char **names = reader->tbx_idx ? tbx_seqnames(reader->tbx_idx, &n) : bcf_hdr_seqnames(reader->header, &n); + for (i=0; i<n; i++) + { + if ( !files->regions ) + files->regions = _regions_init_string(names[i]); + else + _regions_add(files->regions, names[i], -1, -1); + } + free(names); + } + + return 1; +} + +bcf_srs_t *bcf_sr_init(void) +{ + bcf_srs_t *files = (bcf_srs_t*) calloc(1,sizeof(bcf_srs_t)); + return files; +} + +static void bcf_sr_destroy1(bcf_sr_t *reader) +{ + 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); + free(files); +} + +void bcf_sr_remove_reader(bcf_srs_t *files, int i) +{ + assert( !files->samples ); // not ready for this yet + 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--; +} + + +/* + Removes duplicate records from the buffer. The meaning of "duplicate" is + controlled by the $collapse variable, which can cause that from multiple + <indel|snp|any> lines only the first is considered and the rest is ignored. + The removal is done by setting the redundant lines' positions to -1 and + moving these lines at the end of the buffer. + */ +static void collapse_buffer(bcf_srs_t *files, bcf_sr_t *reader) +{ + int irec,jrec, has_snp=0, has_indel=0, has_any=0; + for (irec=1; irec<=reader->nbuffer; irec++) + { + bcf1_t *line = reader->buffer[irec]; + if ( line->pos != reader->buffer[1]->pos ) break; + if ( files->collapse&COLLAPSE_ANY ) + { + if ( !has_any ) has_any = 1; + else line->pos = -1; + } + int line_type = bcf_get_variant_types(line); + if ( files->collapse&COLLAPSE_SNPS && line_type&(VCF_SNP|VCF_MNP) ) + { + if ( !has_snp ) has_snp = 1; + else line->pos = -1; + } + if ( files->collapse&COLLAPSE_INDELS && line_type&VCF_INDEL ) + { + if ( !has_indel ) has_indel = 1; + else line->pos = -1; + } + } + bcf1_t *tmp; + irec = jrec = 1; + while ( irec<=reader->nbuffer && jrec<=reader->nbuffer ) + { + if ( reader->buffer[irec]->pos != -1 ) { irec++; continue; } + if ( jrec<=irec ) jrec = irec+1; + while ( jrec<=reader->nbuffer && reader->buffer[jrec]->pos==-1 ) jrec++; + if ( jrec<=reader->nbuffer ) + { + tmp = reader->buffer[irec]; reader->buffer[irec] = reader->buffer[jrec]; reader->buffer[jrec] = tmp; + } + } + reader->nbuffer = irec - 1; +} + +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,"%s%s\t%s:%d\t%s ", 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"); +} + +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, int start, int end) +{ + if ( end>=MAX_CSI_COOR ) + { + fprintf(stderr,"The coordinate is out of csi index limit: %d\n", 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); + } + assert(reader->itr); + 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 + if ( bcf_sr_regions_next(files->regions)<0 ) return -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; +} + +/* + * _reader_fill_buffer() - buffers all records with the same coordinate + */ +static void _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; + + // No iterator (sequence not present in this file) and not streaming + if ( !reader->itr && !files->streaming ) return; + + // 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 ) + { + if ( (ret=hts_getline(reader->file, KS_SEP_LINE, &files->tmps)) < 0 ) break; // no more lines + int ret = vcf_parse1(&files->tmps, reader->header, reader->buffer[reader->nbuffer+1]); + if ( ret<0 ) break; + } + else if ( reader->file->format.format==bcf ) + { + if ( (ret=bcf_read1(reader->file, reader->header, reader->buffer[reader->nbuffer+1])) < 0 ) break; // no more lines + } + else + { + fprintf(stderr,"[%s:%d %s] fixme: not ready for this\n", __FILE__,__LINE__,__FUNCTION__); + exit(1); + } + } + else if ( reader->tbx_idx ) + { + if ( (ret=tbx_itr_next(reader->file, reader->tbx_idx, reader->itr, &files->tmps)) < 0 ) break; // no more lines + vcf_parse1(&files->tmps, reader->header, reader->buffer[reader->nbuffer+1]); + } + else + { + if ( (ret=bcf_itr_next(reader->file, reader->itr, reader->buffer[reader->nbuffer+1])) < 0 ) break; // no more lines + bcf_subset_format(reader->header,reader->buffer[reader->nbuffer+1]); + } + + // 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]->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->collapse && reader->nbuffer>=2 && reader->buffer[1]->pos==reader->buffer[2]->pos ) + collapse_buffer(files, reader); +} + +/* + * _readers_shift_buffer() - removes the first line and all subsequent lines with the same position + */ +static void _reader_shift_buffer(bcf_sr_t *reader) +{ + int i; + for (i=2; i<=reader->nbuffer; i++) + if ( reader->buffer[i]->pos!=reader->buffer[1]->pos ) break; + if ( i<=reader->nbuffer ) + { + // A record with a different position follows, swap it. Because of the reader's logic, + // only one such line can be present. + bcf1_t *tmp = reader->buffer[1]; reader->buffer[1] = reader->buffer[i]; reader->buffer[i] = tmp; + reader->nbuffer = 1; + } + else + reader->nbuffer = 0; // no other line +} + +/* + * _reader_match_alleles() - from multiple buffered lines selects the one which + * corresponds best to the template line. The logic is controlled by COLLAPSE_* + * Returns 0 on success or -1 when no good matching line is found. + */ +static int _reader_match_alleles(bcf_srs_t *files, bcf_sr_t *reader, bcf1_t *tmpl) +{ + int i, irec = -1; + + // if no template given, use the first available record + if ( !tmpl ) + irec = 1; + else + { + int tmpl_type = bcf_get_variant_types(tmpl); + for (i=1; i<=reader->nbuffer; i++) + { + bcf1_t *line = reader->buffer[i]; + if ( line->pos != reader->buffer[1]->pos ) break; // done with this reader + + // Easiest case: matching by position only + if ( files->collapse&COLLAPSE_ANY ) { irec=i; break; } + + int line_type = bcf_get_variant_types(line); + + // No matter what the alleles are, as long as they are both SNPs + if ( files->collapse&COLLAPSE_SNPS && tmpl_type&VCF_SNP && line_type&VCF_SNP ) { irec=i; break; } + // ... or indels + if ( files->collapse&COLLAPSE_INDELS && tmpl_type&VCF_INDEL && line_type&VCF_INDEL ) { irec=i; break; } + + // More thorough checking: REFs must match + if ( tmpl->rlen != line->rlen ) continue; // different length + if ( strcmp(tmpl->d.allele[0], line->d.allele[0]) ) continue; // the strings do not match + + int ial,jal; + if ( files->collapse==COLLAPSE_NONE ) + { + // Exact match, all alleles must be identical + if ( tmpl->n_allele!=line->n_allele ) continue; // different number of alleles, skip + + int nmatch = 1; // REF has been already checked + for (ial=1; ial<tmpl->n_allele; ial++) + { + for (jal=1; jal<line->n_allele; jal++) + if ( !strcmp(tmpl->d.allele[ial], line->d.allele[jal]) ) { nmatch++; break; } + } + if ( nmatch==tmpl->n_allele ) { irec=i; break; } // found: exact match + continue; + } + + if ( line->n_allele==1 && tmpl->n_allele==1 ) { irec=i; break; } // both sites are non-variant + + // COLLAPSE_SOME: at least some ALTs must match + for (ial=1; ial<tmpl->n_allele; ial++) + { + for (jal=1; jal<line->n_allele; jal++) + if ( !strcmp(tmpl->d.allele[ial], line->d.allele[jal]) ) { irec=i; break; } + if ( irec>=1 ) break; + } + if ( irec>=1 ) break; + } + if ( irec==-1 ) return -1; // no matching line was found + } + + // Set the selected line (irec) as active: set it to buffer[0], move the remaining lines forward + // and put the old bcf1_t record at the end. + bcf1_t *tmp = reader->buffer[0]; + reader->buffer[0] = reader->buffer[irec]; + for (i=irec+1; i<=reader->nbuffer; i++) reader->buffer[i-1] = reader->buffer[i]; + reader->buffer[ reader->nbuffer ] = tmp; + reader->nbuffer--; + + return 0; +} + +int _reader_next_line(bcf_srs_t *files) +{ + int i, min_pos = INT_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 + const char *chr = NULL; + for (i=0; i<files->nreaders; i++) + { + _reader_fill_buffer(files, &files->readers[i]); + + // Update the minimum coordinate + if ( !files->readers[i].nbuffer ) continue; + 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]); + } + } + if ( min_pos==INT_MAX ) + { + if ( !files->regions ) break; + continue; + } + + // Skip this position if not present in targets + if ( files->targets ) + { + int ret = bcf_sr_regions_overlap(files->targets, chr, min_pos, min_pos); + if ( (!files->targets_exclude && ret<0) || (files->targets_exclude && !ret) ) + { + // Remove all lines with this position from the buffer + for (i=0; i<files->nreaders; i++) + if ( files->readers[i].nbuffer && files->readers[i].buffer[1]->pos==min_pos ) + _reader_shift_buffer(&files->readers[i]); + min_pos = INT_MAX; + continue; + } + } + + break; // done: min_pos is set + } + + // There can be records with duplicate positions. Set the active line intelligently so that + // the alleles match. + int nret = 0; // number of readers sharing the position + bcf1_t *first = NULL; // record which will be used for allele matching + for (i=0; i<files->nreaders; i++) + { + files->has_line[i] = 0; + + // Skip readers with no records at this position + if ( !files->readers[i].nbuffer || files->readers[i].buffer[1]->pos!=min_pos ) continue; + + // Until now buffer[0] of all reader was empty and the lines started at buffer[1]. + // Now lines which are ready to be output will be moved to buffer[0]. + if ( _reader_match_alleles(files, &files->readers[i], first) < 0 ) continue; + if ( !first ) first = files->readers[i].buffer[0]; + + nret++; + files->has_line[i] = 1; + } + return nret; +} + +int bcf_sr_next_line(bcf_srs_t *files) +{ + if ( !files->targets_als ) + return _reader_next_line(files); + + while (1) + { + int i, ret = _reader_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; +} + + +int bcf_sr_seek(bcf_srs_t *readers, const char *seq, int pos) +{ + if ( !seq && !pos ) + { + // seek to start + bcf_sr_seek_start(readers); + return 0; + } + + bcf_sr_regions_overlap(readers->regions, seq, pos, pos); + int i, nret = 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 ) + { + 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; +} + +// Add a new region into a list sorted by start,end. On input the coordinates +// are 1-based, stored 0-based, inclusive. +static void _regions_add(bcf_sr_regions_t *reg, const char *chr, int start, int 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 + iseq = reg->nseqs++; + reg->seq_names = (char**) realloc(reg->seq_names,sizeof(char*)*reg->nseqs); + reg->regs = (region_t*) realloc(reg->regs,sizeof(region_t)*reg->nseqs); + memset(®->regs[reg->nseqs-1],0,sizeof(region_t)); + reg->seq_names[iseq] = strdup(chr); + reg->regs[iseq].creg = -1; + khash_str2int_set(reg->seq_hash,reg->seq_names[iseq],iseq); + } + + region_t *creg = ®->regs[iseq]; + + // the regions may not be sorted on input: binary search + int i, min = 0, max = creg->nregs - 1; + while ( min<=max ) + { + i = (max+min)/2; + if ( start < creg->regs[i].start ) max = i - 1; + else if ( start > creg->regs[i].start ) min = i + 1; + else break; + } + if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end ) + { + // no such region, insert a new one just after max + hts_expand(region1_t,creg->nregs+1,creg->mregs,creg->regs); + if ( ++max < creg->nregs ) + memmove(&creg->regs[max+1],&creg->regs[max],(creg->nregs - max)*sizeof(region1_t)); + creg->regs[max].start = start; + creg->regs[max].end = end; + creg->nregs++; + } +} + +// File name or a list of genomic locations. If file name, NULL is returned. +static bcf_sr_regions_t *_regions_init_string(const char *str) +{ + bcf_sr_regions_t *reg = (bcf_sr_regions_t *) calloc(1, sizeof(bcf_sr_regions_t)); + reg->start = reg->end = -1; + reg->prev_start = reg->prev_seq = -1; + + kstring_t tmp = {0,0,0}; + const char *sp = str, *ep = str; + int from, to; + while ( 1 ) + { + while ( *ep && *ep!=',' && *ep!=':' ) ep++; + tmp.l = 0; + kputsn(sp,ep-sp,&tmp); + if ( *ep==':' ) + { + sp = ep+1; + from = strtol(sp,(char**)&ep,10); + if ( sp==ep ) + { + fprintf(stderr,"[%s:%d %s] Could not parse the region(s): %s\n", __FILE__,__LINE__,__FUNCTION__,str); + free(reg); free(tmp.s); return NULL; + } + if ( !*ep || *ep==',' ) + { + _regions_add(reg, tmp.s, from, from); + sp = ep; + continue; + } + if ( *ep!='-' ) + { + fprintf(stderr,"[%s:%d %s] Could not parse the region(s): %s\n", __FILE__,__LINE__,__FUNCTION__,str); + free(reg); free(tmp.s); return NULL; + } + ep++; + sp = ep; + to = strtol(sp,(char**)&ep,10); + if ( *ep && *ep!=',' ) + { + fprintf(stderr,"[%s:%d %s] Could not parse the region(s): %s\n", __FILE__,__LINE__,__FUNCTION__,str); + free(reg); free(tmp.s); return NULL; + } + if ( sp==ep ) to = MAX_CSI_COOR-1; + _regions_add(reg, tmp.s, from, to); + if ( !*ep ) break; + sp = ep; + } + else + { + if ( tmp.l ) _regions_add(reg, tmp.s, -1, -1); + if ( !*ep ) break; + sp = ++ep; + } + } + free(tmp.s); + return reg; +} + +// ichr,ifrom,ito are 0-based; +// returns -1 on error, 0 if the line is a comment line, 1 on success +static int _regions_parse_line(char *line, int ichr,int ifrom,int ito, char **chr,char **chr_end,int *from,int *to) +{ + *chr_end = NULL; + + if ( line[0]=='#' ) return 0; + + int k,l; // index of the start and end column of the tab-delimited file + if ( ifrom <= ito ) + k = ifrom, l = ito; + else + l = ifrom, k = ito; + + int i; + char *se = line, *ss = NULL; // start and end + char *tmp; + for (i=0; i<=k && *se; i++) + { + ss = i==0 ? se++ : ++se; + while (*se && *se!='\t') se++; + } + if ( i<=k ) return -1; + if ( k==l ) + { + *from = *to = strtol(ss, &tmp, 10); + if ( tmp==ss ) return -1; + } + else + { + if ( k==ifrom ) + *from = strtol(ss, &tmp, 10); + else + *to = strtol(ss, &tmp, 10); + if ( ss==tmp ) return -1; + + for (i=k; i<l && *se; i++) + { + ss = ++se; + while (*se && *se!='\t') se++; + } + if ( i<l ) return -1; + if ( k==ifrom ) + *to = strtol(ss, &tmp, 10); + else + *from = strtol(ss, &tmp, 10); + if ( ss==tmp ) return -1; + } + + ss = se = line; + for (i=0; i<=ichr && *se; i++) + { + if ( i>0 ) ss = ++se; + while (*se && *se!='\t') se++; + } + if ( i<=ichr ) return -1; + *chr_end = se; + *chr = ss; + return 1; +} + +bcf_sr_regions_t *bcf_sr_regions_init(const char *regions, int is_file, int ichr, int ifrom, int ito) +{ + bcf_sr_regions_t *reg; + if ( !is_file ) return _regions_init_string(regions); + + reg = (bcf_sr_regions_t *) calloc(1, sizeof(bcf_sr_regions_t)); + reg->start = reg->end = -1; + reg->prev_start = reg->prev_seq = -1; + + reg->file = hts_open(regions, "rb"); + if ( !reg->file ) + { + fprintf(stderr,"[%s:%d %s] Could not open file: %s\n", __FILE__,__LINE__,__FUNCTION__,regions); + free(reg); + return NULL; + } + + reg->tbx = tbx_index_load(regions); + if ( !reg->tbx ) + { + int len = strlen(regions); + int is_bed = strcasecmp(".bed",regions+len-4) ? 0 : 1; + if ( !is_bed && !strcasecmp(".bed.gz",regions+len-7) ) is_bed = 1; + + if ( reg->file->format.format==vcf ) ito = 1; + + // read the whole file, tabix index is not present + while ( hts_getline(reg->file, KS_SEP_LINE, ®->line) > 0 ) + { + char *chr, *chr_end; + int from, to, ret; + ret = _regions_parse_line(reg->line.s, ichr,ifrom,abs(ito), &chr,&chr_end,&from,&to); + if ( ret < 0 ) + { + if ( ito<0 ) + ret = _regions_parse_line(reg->line.s, ichr,ifrom,ifrom, &chr,&chr_end,&from,&to); + if ( ret<0 ) + { + fprintf(stderr,"[%s:%d] Could not parse the file %s, using the columns %d,%d[,%d]\n", __FILE__,__LINE__,regions,ichr+1,ifrom+1,ito+1); + hts_close(reg->file); reg->file = NULL; free(reg); + return NULL; + } + } + if ( !ret ) continue; + if ( is_bed ) from++; + *chr_end = 0; + _regions_add(reg, chr, from, to); + *chr_end = '\t'; + } + hts_close(reg->file); reg->file = NULL; + if ( !reg->nseqs ) { free(reg); return NULL; } + return reg; + } + + reg->seq_names = (char**) tbx_seqnames(reg->tbx, ®->nseqs); + if ( !reg->seq_hash ) + reg->seq_hash = khash_str2int_init(); + int i; + for (i=0; i<reg->nseqs; i++) + { + khash_str2int_set(reg->seq_hash,reg->seq_names[i],i); + } + reg->fname = strdup(regions); + reg->is_bin = 1; + return reg; +} + +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_regions_seek(bcf_sr_regions_t *reg, const char *seq) +{ + reg->iseq = reg->start = reg->end = -1; + if ( khash_str2int_get(reg->seq_hash, seq, ®->iseq) < 0 ) return -1; // sequence seq not in regions + + // using in-memory regions + if ( reg->regs ) + { + reg->regs[reg->iseq].creg = -1; + return 0; + } + + // reading regions from tabix + if ( reg->itr ) tbx_itr_destroy(reg->itr); + reg->itr = tbx_itr_querys(reg->tbx, seq); + if ( reg->itr ) return 0; + + return -1; +} + +int bcf_sr_regions_next(bcf_sr_regions_t *reg) +{ + if ( reg->iseq<0 ) return -1; + reg->start = reg->end = -1; + reg->nals = 0; + + // using in-memory regions + if ( reg->regs ) + { + while ( reg->iseq < reg->nseqs ) + { + reg->regs[reg->iseq].creg++; + if ( reg->regs[reg->iseq].creg < reg->regs[reg->iseq].nregs ) break; + reg->iseq++; + } + if ( reg->iseq >= reg->nseqs ) { reg->iseq = -1; return -1; } // no more regions left + region1_t *creg = ®->regs[reg->iseq].regs[reg->regs[reg->iseq].creg]; + reg->start = creg->start; + reg->end = creg->end; + return 0; + } + + // reading from tabix + char *chr, *chr_end; + int ichr = 0, ifrom = 1, ito = 2, is_bed = 0, from, to; + if ( reg->tbx ) + { + ichr = reg->tbx->conf.sc-1; + ifrom = reg->tbx->conf.bc-1; + ito = reg->tbx->conf.ec-1; + if ( ito<0 ) ito = ifrom; + is_bed = reg->tbx->conf.preset==TBX_UCSC ? 1 : 0; + } + + int ret = 0; + while ( !ret ) + { + if ( reg->itr ) + { + // tabix index present, reading a chromosome block + ret = tbx_itr_next(reg->file, reg->tbx, reg->itr, ®->line); + if ( ret<0 ) { reg->iseq = -1; return -1; } + } + else + { + if ( reg->is_bin ) + { + // Waited for seek which never came. Reopen in text mode and stream + // through the regions, otherwise hts_getline would fail + hts_close(reg->file); + reg->file = hts_open(reg->fname, "r"); + if ( !reg->file ) + { + fprintf(stderr,"[%s:%d %s] Could not open file: %s\n", __FILE__,__LINE__,__FUNCTION__,reg->fname); + reg->file = NULL; + bcf_sr_regions_destroy(reg); + return -1; + } + reg->is_bin = 0; + } + + // tabix index absent, reading the whole file + ret = hts_getline(reg->file, KS_SEP_LINE, ®->line); + if ( ret<0 ) { reg->iseq = -1; return -1; } + } + ret = _regions_parse_line(reg->line.s, ichr,ifrom,ito, &chr,&chr_end,&from,&to); + if ( ret<0 ) + { + fprintf(stderr,"[%s:%d] Could not parse the file %s, using the columns %d,%d,%d\n", __FILE__,__LINE__,reg->fname,ichr+1,ifrom+1,ito+1); + return -1; + } + } + if ( is_bed ) from++; + + *chr_end = 0; + if ( khash_str2int_get(reg->seq_hash, chr, ®->iseq)<0 ) + { + fprintf(stderr,"Broken tabix index? The sequence \"%s\" not in dictionary [%s]\n", chr,reg->line.s); + exit(1); + } + *chr_end = '\t'; + + reg->start = from - 1; + reg->end = to - 1; + return 0; +} + +static int _regions_match_alleles(bcf_sr_regions_t *reg, int als_idx, bcf1_t *rec) +{ + int i = 0, max_len = 0; + if ( !reg->nals ) + { + char *ss = reg->line.s; + while ( i<als_idx && *ss ) + { + if ( *ss=='\t' ) i++; + ss++; + } + char *se = ss; + reg->nals = 1; + while ( *se && *se!='\t' ) + { + if ( *se==',' ) reg->nals++; + se++; + } + ks_resize(®->als_str, se-ss+1+reg->nals); + reg->als_str.l = 0; + hts_expand(char*,reg->nals,reg->mals,reg->als); + reg->nals = 0; + + se = ss; + while ( *(++se) ) + { + if ( *se=='\t' ) break; + if ( *se!=',' ) continue; + reg->als[reg->nals] = ®->als_str.s[reg->als_str.l]; + kputsn(ss,se-ss,®->als_str); + if ( ®->als_str.s[reg->als_str.l] - reg->als[reg->nals] > max_len ) max_len = ®->als_str.s[reg->als_str.l] - reg->als[reg->nals]; + reg->als_str.l++; + reg->nals++; + ss = ++se; + } + reg->als[reg->nals] = ®->als_str.s[reg->als_str.l]; + kputsn(ss,se-ss,®->als_str); + if ( ®->als_str.s[reg->als_str.l] - reg->als[reg->nals] > max_len ) max_len = ®->als_str.s[reg->als_str.l] - reg->als[reg->nals]; + reg->nals++; + reg->als_type = max_len > 1 ? VCF_INDEL : VCF_SNP; // this is a simplified check, see vcf.c:bcf_set_variant_types + } + int type = bcf_get_variant_types(rec); + if ( reg->als_type & VCF_INDEL ) + return type & VCF_INDEL ? 1 : 0; + return !(type & VCF_INDEL) ? 1 : 0; +} + +int bcf_sr_regions_overlap(bcf_sr_regions_t *reg, const char *seq, int start, int end) +{ + int iseq; + if ( khash_str2int_get(reg->seq_hash, seq, &iseq)<0 ) return -1; // no such sequence + + if ( reg->prev_seq==-1 || iseq!=reg->prev_seq || reg->prev_start > start ) // new chromosome or after a seek + { + // flush regions left on previous chromosome + if ( reg->missed_reg_handler && reg->prev_seq!=-1 && reg->iseq!=-1 ) + bcf_sr_regions_flush(reg); + + bcf_sr_regions_seek(reg, seq); + reg->start = reg->end = -1; + } + if ( reg->prev_seq==iseq && reg->iseq!=iseq ) return -2; // no more regions on this chromosome + reg->prev_seq = reg->iseq; + reg->prev_start = start; + + while ( iseq==reg->iseq && reg->end < start ) + { + if ( bcf_sr_regions_next(reg) < 0 ) return -2; // no more regions left + if ( reg->iseq != iseq ) return -1; // does not overlap any regions + if ( reg->missed_reg_handler && reg->end < start ) reg->missed_reg_handler(reg, reg->missed_reg_data); + } + if ( reg->start <= end ) return 0; // region overlap + return -1; // no overlap +} + +void bcf_sr_regions_flush(bcf_sr_regions_t *reg) +{ + if ( !reg->missed_reg_handler || reg->prev_seq==-1 ) return; + while ( !bcf_sr_regions_next(reg) ) reg->missed_reg_handler(reg, reg->missed_reg_data); + return; +} +