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vcfmerge.c
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/* vcfmerge.c -- Merge multiple VCF/BCF files to create one multi-sample file.
Copyright (C) 2012-2019 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 <string.h>
#include <strings.h>
#include <errno.h>
#include <unistd.h>
#include <getopt.h>
#include <htslib/vcf.h>
#include <htslib/synced_bcf_reader.h>
#include <htslib/vcfutils.h>
#include <htslib/faidx.h>
#include <math.h>
#include <ctype.h>
#include <time.h>
#include "bcftools.h"
#include "regidx.h"
#include "vcmp.h"
#define DBG 0
#include <htslib/khash.h>
KHASH_MAP_INIT_STR(strdict, int)
typedef khash_t(strdict) strdict_t;
#define FLT_LOGIC_ADD 0
#define FLT_LOGIC_REMOVE 1
#define SKIP_DONE 1 // the record was processed
#define SKIP_DIFF 2 // not compatible, merge later
#define IS_VL_G(hdr,id) (bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_G)
#define IS_VL_A(hdr,id) (bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_A)
#define IS_VL_R(hdr,id) (bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_R)
#define SWAP(type_t,a,b) { type_t tmp = (a); (a) = (b); (b) = tmp; }
// For merging INFO Number=A,G,R tags
typedef struct
{
const char *hdr_tag;
int type, nvals;
int nbuf, mbuf;
uint8_t *buf;
}
AGR_info_t;
// Rules for merging arbitrary INFO tags
typedef struct _info_rule_t
{
char *hdr_tag;
void (*merger)(bcf_hdr_t *hdr, bcf1_t *line, struct _info_rule_t *rule);
int type; // one of BCF_HT_*
int block_size; // number of values in a block
int type_size; // size of the corresponding BCF_HT_* type
int nblocks; // number of blocks in nvals (the number of merged files)
int nvals, mvals; // used and total size of vals array
void *vals; // the info tag values
}
info_rule_t;
typedef struct
{
bcf1_t *line;
int end, active; // end: 0-based INFO/END
}
gvcf_aux_t;
// Auxiliary merge data for selecting the right combination
// of buffered records across multiple readers. maux1_t
// corresponds to one buffered line.
typedef struct
{
int skip;
int *map; // mapping from input alleles to the array of output alleles (set by merge_alleles)
int mmap; // size of map array (only buffer[i].n_allele is actually used)
int als_differ;
}
maux1_t;
typedef struct
{
int rid; // current rid
int beg,end; // valid ranges in reader's buffer [beg,end). Maintained by maux_reset and gvcf_flush.
int cur; // current line or -1 if none
int mrec; // allocated size of buf
maux1_t *rec; // buffer to keep reader's lines
bcf1_t **lines; // source buffer: either gvcf or readers' buffer
}
buffer_t;
typedef struct
{
int n, pos, var_types; // number of readers, current position, currently available variant types
char *chr; // current chromosome
char **als, **out_als; // merged alleles (temp, may contain empty records) and merged alleles ready for output
int nals, mals, nout_als, mout_als; // size of the output array
int *cnt, ncnt; // number of records that refer to the alleles
int *smpl_ploidy, *smpl_nGsize; // ploidy and derived number of values in Number=G tags, updated for each line (todo: cache for missing cases)
bcf_fmt_t **fmt_map; // i-th output FORMAT field corresponds in j-th reader to i*nreader+j, first row is reserved for GT
int nfmt_map; // number of rows in the fmt_map array
int *agr_map, nagr_map, magr_map; // mapping between Number=AGR element indexes
void *tmp_arr;
size_t ntmp_arr;
buffer_t *buf;
AGR_info_t *AGR_info;
int nAGR_info, mAGR_info;
bcf_srs_t *files;
int gvcf_min, // min buffered gvcf END position (NB: gvcf_min is 1-based) or 0 if no active lines are present
gvcf_break; // 0-based position of a next record which breaks a gVCF block
gvcf_aux_t *gvcf; // buffer of gVCF lines, for each reader one line
int nout_smpl;
kstring_t *str;
}
maux_t;
typedef struct
{
vcmp_t *vcmp;
maux_t *maux;
regidx_t *regs; // apply regions only after the blocks are expanded
regitr_t *regs_itr;
int header_only, collapse, output_type, force_samples, merge_by_id, do_gvcf, filter_logic, missing_to_ref;
char *header_fname, *output_fname, *regions_list, *info_rules, *file_list;
faidx_t *gvcf_fai;
info_rule_t *rules;
int nrules;
strdict_t *tmph;
kstring_t tmps;
bcf_srs_t *files;
bcf1_t *out_line;
htsFile *out_fh;
bcf_hdr_t *out_hdr;
char **argv;
int argc, n_threads, record_cmd_line;
}
args_t;
static bcf1_t *maux_get_line(args_t *args, int i)
{
maux_t *ma = args->maux;
int ibuf = ma->buf[i].cur;
if ( ibuf >= 0 ) return ma->buf[i].lines[ibuf];
return NULL;
}
static void info_rules_merge_sum(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule)
{
if ( !rule->nvals ) return;
int i, j, ndim = rule->block_size;
#define BRANCH(type_t,is_missing) { \
type_t *ptr = (type_t*) rule->vals; \
for (i=0; i<rule->nvals; i++) if ( is_missing ) ptr[i] = 0; \
for (i=1; i<rule->nblocks; i++) \
{ \
for (j=0; j<ndim; j++) ptr[j] += ptr[j+i*ndim]; \
} \
}
switch (rule->type) {
case BCF_HT_INT: BRANCH(int32_t, ptr[i]==bcf_int32_missing); break;
case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i])); break;
default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type);
}
#undef BRANCH
bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type);
}
static void info_rules_merge_avg(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule)
{
if ( !rule->nvals ) return;
int i, j, ndim = rule->block_size;
#define BRANCH(type_t,is_missing) { \
type_t *ptr = (type_t*) rule->vals; \
for (i=0; i<rule->nvals; i++) if ( is_missing ) ptr[i] = 0; \
for (j=0; j<ndim; j++) \
{ \
double sum = 0; \
for (i=0; i<rule->nblocks; i++) sum += ptr[j+i*ndim]; \
ptr[j] = sum / rule->nblocks; \
} \
}
switch (rule->type) {
case BCF_HT_INT: BRANCH(int32_t, ptr[i]==bcf_int32_missing); break;
case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i])); break;
default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type);
}
#undef BRANCH
bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type);
}
static void info_rules_merge_min(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule)
{
if ( !rule->nvals ) return;
int i, j, ndim = rule->block_size;
#define BRANCH(type_t,is_missing,set_missing,huge_val) { \
type_t *ptr = (type_t*) rule->vals; \
for (i=0; i<rule->nvals; i++) if ( is_missing ) ptr[i] = huge_val; \
for (i=1; i<rule->nblocks; i++) \
{ \
for (j=0; j<ndim; j++) if ( ptr[j] > ptr[j+i*ndim] ) ptr[j] = ptr[j+i*ndim]; \
} \
for (i=0; i<rule->nvals; i++) if ( ptr[i]==huge_val ) set_missing; \
}
switch (rule->type) {
case BCF_HT_INT: BRANCH(int32_t, ptr[i]==bcf_int32_missing, ptr[i]=bcf_int32_missing, INT32_MAX); break;
case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i]), bcf_float_set_missing(ptr[i]), HUGE_VAL); break;
default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type);
}
#undef BRANCH
bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type);
}
static void info_rules_merge_max(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule)
{
if ( !rule->nvals ) return;
int i, j, ndim = rule->block_size;
#define BRANCH(type_t,is_missing,set_missing,huge_val) { \
type_t *ptr = (type_t*) rule->vals; \
for (i=0; i<rule->nvals; i++) if ( is_missing ) ptr[i] = huge_val; \
for (i=1; i<rule->nblocks; i++) \
{ \
for (j=0; j<ndim; j++) if ( ptr[j] < ptr[j+i*ndim] ) ptr[j] = ptr[j+i*ndim]; \
} \
for (i=0; i<rule->nvals; i++) if ( ptr[i]==huge_val ) set_missing; \
}
switch (rule->type) {
case BCF_HT_INT: BRANCH(int32_t, ptr[i]==bcf_int32_missing, ptr[i]=bcf_int32_missing, INT32_MIN); break;
case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i]), bcf_float_set_missing(ptr[i]), -HUGE_VAL); break;
default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type);
}
#undef BRANCH
bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type);
}
static void info_rules_merge_join(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule)
{
if ( !rule->nvals ) return;
if ( rule->type==BCF_HT_STR )
{
((char*)rule->vals)[rule->nvals] = 0;
bcf_update_info_string(hdr,line,rule->hdr_tag,rule->vals);
}
else
bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,rule->nvals,rule->type);
}
static int info_rules_comp_key2(const void *a, const void *b)
{
info_rule_t *rule1 = (info_rule_t*) a;
info_rule_t *rule2 = (info_rule_t*) b;
return strcmp(rule1->hdr_tag, rule2->hdr_tag);
}
static int info_rules_comp_key(const void *a, const void *b)
{
char *key = (char*) a;
info_rule_t *rule = (info_rule_t*) b;
return strcmp(key, rule->hdr_tag);
}
static void info_rules_init(args_t *args)
{
if ( args->info_rules && !strcmp("-",args->info_rules) ) return;
kstring_t str = {0,0,0};
if ( !args->info_rules )
{
if ( bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "DP")) ) kputs("DP:sum",&str);
if ( bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "DP4")) )
{
if ( str.l ) kputc(',',&str);
kputs("DP4:sum",&str);
}
if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "QS")) )
{
if ( str.l ) kputc(',',&str);
kputs("QS:sum",&str);
}
if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "MinDP")) )
{
if ( str.l ) kputc(',',&str);
kputs("MinDP:min",&str);
}
if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "I16")) )
{
if ( str.l ) kputc(',',&str);
kputs("I16:sum",&str);
}
if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "IDV")) )
{
if ( str.l ) kputc(',',&str);
kputs("IDV:max",&str);
}
if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "IMF")) )
{
if ( str.l ) kputc(',',&str);
kputs("IMF:max",&str);
}
if ( !str.l ) return;
args->info_rules = str.s;
}
args->nrules = 1;
char *ss = strdup(args->info_rules), *tmp = ss;
int n = 0;
while ( *ss )
{
if ( *ss==':' ) { *ss = 0; n++; if ( n%2==0 ) error("Could not parse INFO rules: \"%s\"\n", args->info_rules); }
else if ( *ss==',' ) { *ss = 0; args->nrules++; n++; if ( n%2==1 ) error("Could not parse INFO rules: \"%s\"\n", args->info_rules); }
ss++;
}
if ( n%2==0 ) error("Could not parse INFO rules: \"%s\"\n", args->info_rules);
args->rules = (info_rule_t*) calloc(args->nrules,sizeof(info_rule_t));
n = 0;
ss = tmp;
while ( n < args->nrules )
{
info_rule_t *rule = &args->rules[n];
rule->hdr_tag = strdup(ss);
int id = bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, rule->hdr_tag);
if ( !bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,id) ) error("The tag is not defined in the header: \"%s\"\n", rule->hdr_tag);
rule->type = bcf_hdr_id2type(args->out_hdr,BCF_HL_INFO,id);
if ( rule->type==BCF_HT_INT ) rule->type_size = sizeof(int32_t);
else if ( rule->type==BCF_HT_REAL ) rule->type_size = sizeof(float);
else if ( rule->type==BCF_HT_STR ) rule->type_size = sizeof(char);
else error("The type is not supported: \"%s\"\n", rule->hdr_tag);
ss = strchr(ss, '\0'); ss++;
if ( !*ss ) error("Could not parse INFO rules, missing logic of \"%s\"\n", rule->hdr_tag);
int is_join = 0;
if ( !strcasecmp(ss,"sum") ) rule->merger = info_rules_merge_sum;
else if ( !strcasecmp(ss,"avg") ) rule->merger = info_rules_merge_avg;
else if ( !strcasecmp(ss,"min") ) rule->merger = info_rules_merge_min;
else if ( !strcasecmp(ss,"max") ) rule->merger = info_rules_merge_max;
else if ( !strcasecmp(ss,"join") ) { rule->merger = info_rules_merge_join; is_join = 1; }
else error("The rule logic \"%s\" not recognised\n", ss);
if ( !is_join && rule->type==BCF_HT_STR )
error("Numeric operation \"%s\" requested on non-numeric field: %s\n", ss, rule->hdr_tag);
if ( bcf_hdr_id2number(args->out_hdr,BCF_HL_INFO,id)==0xfffff )
{
int is_agr = (
bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)==BCF_VL_A ||
bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)==BCF_VL_G ||
bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)==BCF_VL_R
) ? 1 : 0;
if ( is_join && is_agr )
error("Cannot -i %s:join on Number=[AGR] tags is not supported.\n", rule->hdr_tag);
if ( !is_join && !is_agr )
error("Only fixed-length vectors are supported with -i %s:%s\n", ss, rule->hdr_tag);
}
ss = strchr(ss, '\0'); ss++;
n++;
}
free(str.s);
free(tmp);
qsort(args->rules, args->nrules, sizeof(*args->rules), info_rules_comp_key2);
}
static void info_rules_destroy(args_t *args)
{
int i;
for (i=0; i<args->nrules; i++)
{
info_rule_t *rule = &args->rules[i];
free(rule->hdr_tag);
free(rule->vals);
}
free(args->rules);
}
static void info_rules_reset(args_t *args)
{
int i;
for (i=0; i<args->nrules; i++)
args->rules[i].nblocks = args->rules[i].nvals = args->rules[i].block_size = 0;
}
static int info_rules_add_values(args_t *args, bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule, maux1_t *als, int var_len)
{
int msize = args->maux->ntmp_arr / rule->type_size;
int ret = bcf_get_info_values(hdr, line, rule->hdr_tag, &args->maux->tmp_arr, &msize, rule->type);
if ( ret<=0 ) error("FIXME: error parsing %s at %s:%d .. %d\n", rule->hdr_tag,bcf_seqname(hdr,line),line->pos+1,ret);
args->maux->ntmp_arr = msize * rule->type_size;
rule->nblocks++;
if ( rule->type==BCF_HT_STR )
{
int need_comma = rule->nblocks==1 ? 0 : 1;
hts_expand(char,rule->nvals+ret+need_comma+1,rule->mvals,rule->vals); // 1 for null-termination
char *tmp = (char*) rule->vals + rule->nvals;
if ( rule->nvals>0 ) { *tmp = ','; tmp++; }
strncpy(tmp,(char*)args->maux->tmp_arr,ret);
rule->nvals += ret + need_comma;
return 1;
}
int i, j;
if ( var_len==BCF_VL_A )
{
if ( ret!=line->n_allele-1 ) error("Wrong number of %s fields at %s:%d\n",rule->hdr_tag,bcf_seqname(hdr,line),line->pos+1);
args->maux->nagr_map = ret;
hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map);
// create mapping from source file ALT indexes to dst file indexes
for (i=0; i<ret; i++) args->maux->agr_map[i] = als->map[i+1] - 1;
rule->block_size = args->maux->nout_als - 1;
}
else if ( var_len==BCF_VL_R )
{
if ( ret!=line->n_allele ) error("Wrong number of %s fields at %s:%d\n",rule->hdr_tag,bcf_seqname(hdr,line),line->pos+1);
args->maux->nagr_map = ret;
hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map);
for (i=0; i<ret; i++) args->maux->agr_map[i] = als->map[i];
rule->block_size = args->maux->nout_als;
}
else if ( var_len==BCF_VL_G )
{
args->maux->nagr_map = bcf_alleles2gt(line->n_allele-1,line->n_allele-1)+1;
assert( ret==line->n_allele || ret==args->maux->nagr_map );
if ( ret==line->n_allele ) // haploid
{
args->maux->nagr_map = line->n_allele;
hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map);
for (i=0; i<ret; i++) args->maux->agr_map[i] = als->map[i];
rule->block_size = args->maux->nout_als;
}
else
{
hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map);
int k_src = 0;
for (i=0; i<line->n_allele; i++)
{
for (j=0; j<=i; j++)
{
args->maux->agr_map[k_src] = bcf_alleles2gt(als->map[i],als->map[j]);
k_src++;
}
}
rule->block_size = bcf_alleles2gt(args->maux->nout_als-1,args->maux->nout_als-1)+1;
}
}
else
{
if ( rule->nblocks>1 && ret!=rule->block_size )
error("Mismatch in number of values for INFO/%s at %s:%d\n", rule->hdr_tag,bcf_seqname(hdr,line),line->pos+1);
rule->block_size = ret;
args->maux->nagr_map = 0;
}
#define BRANCH(src_type_t,dst_type_t,set_missing) { \
src_type_t *src = (src_type_t *) args->maux->tmp_arr; \
hts_expand0(dst_type_t,(rule->nvals+rule->block_size),rule->mvals,rule->vals); \
dst_type_t *dst = (dst_type_t *) rule->vals + rule->nvals; \
rule->nvals += rule->block_size; \
if ( !args->maux->nagr_map ) \
{ \
for (i=0; i<ret; i++) dst[i] = src[i]; \
} \
else \
{ \
for (i=0; i<rule->block_size; i++) set_missing; \
for (i=0; i<ret; i++) dst[args->maux->agr_map[i]] = src[i]; \
} \
}
switch (rule->type) {
case BCF_HT_INT: BRANCH(int, int32_t, dst[i] = bcf_int32_missing); break;
case BCF_HT_REAL: BRANCH(float, float, bcf_float_set_missing(dst[i])); break;
default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type);
}
#undef BRANCH
return 1;
}
int bcf_hdr_sync(bcf_hdr_t *h);
void merge_headers(bcf_hdr_t *hw, const bcf_hdr_t *hr, const char *clash_prefix, int force_samples)
{
// header lines
hw = bcf_hdr_merge(hw, hr);
// samples
int i;
for (i=0; i<bcf_hdr_nsamples(hr); i++)
{
char *rmme = NULL, *name = hr->samples[i];
while ( bcf_hdr_id2int(hw, BCF_DT_SAMPLE, name)!=-1 )
{
// there is a sample with the same name
if ( !force_samples ) error("Error: Duplicate sample names (%s), use --force-samples to proceed anyway.\n", name);
// Resolve conflicting samples names. For example, replace:
// A + A with A,2:A
// A,2:A + A with A,2:A,2:2:A
int len = strlen(name) + strlen(clash_prefix) + 1;
char *tmp = (char*) malloc(sizeof(char)*(len+1));
sprintf(tmp,"%s:%s",clash_prefix,name);
free(rmme);
rmme = name = tmp;
}
bcf_hdr_add_sample(hw,name);
free(rmme);
}
}
void debug_als(char **als, int nals)
{
int k; for (k=0; k<nals; k++) fprintf(stderr,"%s ", als[k]);
fprintf(stderr,"\n");
}
/**
* normalize_alleles() - create smallest possible representation of the alleles
* @als: alleles to be merged, first is REF (rw)
* @nals: number of $a alleles
*
* Best explained on an example:
* In: REF=GTTT ALT=GTT
* Out: REF=GT ALT=G
*
* Note: the als array will be modified
*/
void normalize_alleles(char **als, int nals)
{
if ( !als[0][1] ) return; // ref is 1base long, we're done
int j, i = 1, done = 0;
int *lens = (int*) malloc(sizeof(int)*nals);
for (j=0; j<nals; j++) lens[j] = strlen(als[j]);
while ( i<lens[0] )
{
for (j=1; j<nals; j++)
{
if ( i>=lens[j] ) done = 1;
if ( als[j][lens[j]-i] != als[0][lens[0]-i] ) { done = 1; break; }
}
if ( done ) break;
i++;
}
if ( i>1 )
{
i--;
als[0][lens[0]-i] = 0;
for (j=1; j<nals; j++) als[j][lens[j]-i] = 0;
}
free(lens);
}
/**
* merge_alleles() - merge two REF,ALT records, $a and $b into $b.
* @a: alleles to be merged, first is REF
* @na: number of $a alleles
* @map: map from the original $a indexes to new $b indexes (0-based)
* @b: alleles to be merged, the array will be expanded as required
* @nb: number of $b alleles
* @mb: size of $b
*
* Returns NULL on error or $b expanded to incorporate $a alleles and sets
* $map. Best explained on an example:
* In: REF ALT
* a: ACG, AC,A (1bp and 2bp deletion)
* b: ACGT, A (3bp deletion)
* Out:
* b: ACGT, A,ACT,AT (3bp, 1bp and 2bp deletion)
* map: 0,2,3
* Here the mapping from the original $a alleles to the new $b alleles is 0->0,
* 1->2, and 2->3.
*/
char **merge_alleles(char **a, int na, int *map, char **b, int *nb, int *mb)
{
// reference allele never changes
map[0] = 0;
int i,j;
int rla = !a[0][1] ? 1 : strlen(a[0]);
int rlb = !b[0][1] ? 1 : strlen(b[0]);
// the most common case: same SNPs
if ( na==2 && *nb==2 && rla==1 && rlb==1 && a[1][0]==b[1][0] && !a[1][1] && !b[1][1] )
{
map[1] = 1;
return b;
}
// Sanity check: reference prefixes must be identical
if ( strncmp(a[0],b[0],rla<rlb?rla:rlb) )
{
if ( strncasecmp(a[0],b[0],rla<rlb?rla:rlb) )
{
fprintf(stderr, "The REF prefixes differ: %s vs %s (%d,%d)\n", a[0],b[0],rla,rlb);
return NULL;
}
// Different case, change to uppercase
for (i=0; i<na; i++)
{
int len = strlen(a[i]);
for (j=0; j<len; j++) a[i][j] = toupper(a[i][j]);
}
for (i=0; i<*nb; i++)
{
int len = strlen(b[i]);
for (j=0; j<len; j++) b[i][j] = toupper(b[i][j]);
}
}
int n = *nb + na;
hts_expand0(char*,n,*mb,b);
// $b alleles need expanding
if ( rla>rlb )
{
for (i=0; i<*nb; i++)
{
if ( b[i][0]=='<' ) continue; // symbolic allele, do not modify
if ( b[i][0]=='*' ) continue; // overlapping deletion (*), do not modify
int l = strlen(b[i]);
b[i] = (char*) realloc(b[i],l+rla-rlb+1);
memcpy(b[i]+l,a[0]+rlb,rla-rlb+1);
}
}
// now check if the $a alleles are present and if not add them
for (i=1; i<na; i++)
{
int const_ai = 1;
char *ai;
if ( rlb>rla && a[i][0]!='<' && a[i][0]!='*' ) // $a alleles need expanding and not a symbolic allele or *
{
int l = strlen(a[i]);
ai = (char*) malloc(l+rlb-rla+1);
memcpy(ai,a[i],l);
memcpy(ai+l,b[0]+rla,rlb-rla+1);
const_ai = 0;
}
else
ai = a[i];
for (j=1; j<*nb; j++)
if ( !strcasecmp(ai,b[j]) ) break;
if ( j<*nb ) // $b already has the same allele
{
map[i] = j;
if ( !const_ai ) free(ai);
continue;
}
// new allele
map[i] = *nb;
b[*nb] = const_ai ? strdup(ai) : ai;
(*nb)++;
}
return b;
}
maux_t *maux_init(args_t *args)
{
bcf_srs_t *files = args->files;
maux_t *ma = (maux_t*) calloc(1,sizeof(maux_t));
ma->n = files->nreaders;
ma->files = files;
int i, n_smpl = 0;
for (i=0; i<ma->n; i++)
n_smpl += bcf_hdr_nsamples(files->readers[i].header);
ma->nout_smpl = n_smpl;
assert( n_smpl==bcf_hdr_nsamples(args->out_hdr) );
if ( args->do_gvcf )
{
ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t));
for (i=0; i<ma->n; i++)
ma->gvcf[i].line = bcf_init1();
}
ma->smpl_ploidy = (int*) calloc(n_smpl,sizeof(int));
ma->smpl_nGsize = (int*) malloc(n_smpl*sizeof(int));
ma->buf = (buffer_t*) calloc(ma->n,sizeof(buffer_t));
for (i=0; i<ma->n; i++)
ma->buf[i].rid = -1;
ma->str = (kstring_t*) calloc(n_smpl,sizeof(kstring_t));
return ma;
}
void maux_destroy(maux_t *ma)
{
int i,j;
for (i=0; i<ma->nout_smpl; i++) free(ma->str[i].s);
free(ma->str);
for (i=0; i<ma->mals; i++)
{
free(ma->als[i]);
ma->als[i] = NULL;
}
for (i=0; i<ma->n; i++) // for each reader
{
for (j=0; j<ma->buf[i].mrec; j++) // for each buffered line
free(ma->buf[i].rec[j].map);
free(ma->buf[i].rec);
}
free(ma->buf);
if ( ma->gvcf )
{
for (i=0; i<ma->n; i++) bcf_destroy(ma->gvcf[i].line);
free(ma->gvcf);
}
for (i=0; i<ma->mAGR_info; i++)
free(ma->AGR_info[i].buf);
free(ma->agr_map);
free(ma->AGR_info);
if (ma->ntmp_arr) free(ma->tmp_arr);
if (ma->nfmt_map) free(ma->fmt_map);
// ma->inf freed in bcf_destroy1
for (i=0; i<ma->mals; i++) free(ma->als[i]);
if (ma->mout_als) free(ma->out_als);
free(ma->als);
free(ma->cnt);
free(ma->smpl_ploidy);
free(ma->smpl_nGsize);
free(ma->chr);
free(ma);
}
void maux_expand1(buffer_t *buf, int size)
{
if ( buf->mrec < size )
{
hts_expand0(maux1_t,size,buf->mrec,buf->rec);
buf->mrec = size;
}
}
void maux_reset(maux_t *ma)
{
int i,j;
for (i=0; i<ma->n; i++) maux_expand1(&ma->buf[i],ma->files->readers[i].nbuffer+1);
for (i=0; i<ma->ncnt; i++) ma->cnt[i] = 0;
for (i=0; i<ma->mals; i++)
{
free(ma->als[i]);
ma->als[i] = NULL;
}
const char *chr = NULL;
ma->nals = 0;
ma->pos = -1;
for (i=0; i<ma->n; i++)
{
if ( !bcf_sr_has_line(ma->files,i) ) continue;
bcf1_t *line = bcf_sr_get_line(ma->files,i);
bcf_hdr_t *hdr = bcf_sr_get_header(ma->files,i);
chr = bcf_seqname(hdr,line);
ma->pos = line->pos;
break;
}
int new_chr = 0;
if ( chr && (!ma->chr || strcmp(ma->chr,chr)) )
{
free(ma->chr);
ma->chr = strdup(chr);
new_chr = 1;
}
for (i=0; i<ma->n; i++)
{
bcf_hdr_t *hdr = bcf_sr_get_header(ma->files,i);
ma->buf[i].rid = bcf_hdr_name2id(hdr,chr);
ma->buf[i].beg = bcf_sr_has_line(ma->files,i) ? 0 : 1;
for (j=ma->buf[i].beg; j<=ma->files->readers[i].nbuffer; j++)
{
ma->buf[i].rec[j].skip = 0;
bcf1_t *line = ma->files->readers[i].buffer[j];
if ( line->rid!=ma->buf[i].rid || line->pos!=ma->pos ) break;
}
ma->buf[i].end = j;
ma->buf[i].cur = -1;
if ( ma->buf[i].beg < ma->buf[i].end )
{
ma->buf[i].lines = ma->files->readers[i].buffer;
if ( ma->gvcf ) ma->gvcf[i].active = 0; // gvcf block cannot overlap with the next record
}
if ( new_chr && ma->gvcf ) ma->gvcf[i].active = 0; // make sure to close active gvcf block on new chr
}
}
void maux_debug(maux_t *ma, int ir, int ib)
{
printf("[%d,%d]\t", ir,ib);
int i;
for (i=0; i<ma->nals; i++)
{
printf(" %s [%d]", ma->als[i], ma->cnt[i]);
}
printf("\n");
}
void merge_chrom2qual(args_t *args, bcf1_t *out)
{
bcf_srs_t *files = args->files;
bcf_hdr_t *out_hdr = args->out_hdr;
int i, ret;
khiter_t kitr;
strdict_t *tmph = args->tmph;
kh_clear(strdict, tmph);
kstring_t *tmps = &args->tmps;
tmps->l = 0;
maux_t *ma = args->maux;
int *al_idxs = (int*) calloc(ma->nals,sizeof(int));
bcf_float_set_missing(out->qual);
// CHROM, POS, ID, QUAL
out->pos = -1;
for (i=0; i<files->nreaders; i++)
{
bcf1_t *line = maux_get_line(args, i);
if ( !line ) continue;
bcf_unpack(line, BCF_UN_ALL);
bcf_sr_t *reader = &files->readers[i];
bcf_hdr_t *hdr = reader->header;
// not all maux alleles are always used, mark the ones we'll need
int j;
for (j=1; j<line->n_allele; j++)
{
int irec = ma->buf[i].cur;
al_idxs[ ma->buf[i].rec[irec].map[j] ] = 1;
}
// position
if ( out->pos==-1 )
{
const char *chr = hdr->id[BCF_DT_CTG][line->rid].key;
out->rid = bcf_hdr_name2id(out_hdr, chr);
if ( strcmp(chr,out_hdr->id[BCF_DT_CTG][out->rid].key) ) error("Uh\n");
out->pos = line->pos;
}
// ID
if ( line->d.id[0]!='.' || line->d.id[1] )
{
kitr = kh_get(strdict, tmph, line->d.id);
if ( kitr == kh_end(tmph) )
{
if ( tmps->l ) kputc(';', tmps);
kputs(line->d.id, tmps);
kh_put(strdict, tmph, line->d.id, &ret);
}
}
// set QUAL to the max qual value. Not exactly correct, but good enough for now
if ( !bcf_float_is_missing(line->qual) )
{
if ( bcf_float_is_missing(out->qual) || out->qual < line->qual ) out->qual = line->qual;
}
}
// set ID
if ( !tmps->l ) kputs(".", tmps);
bcf_update_id(out_hdr, out, tmps->s);
// set alleles
ma->nout_als = 0;
for (i=1; i<ma->nals; i++)
{
if ( !al_idxs[i] ) continue;
ma->nout_als++;
// Adjust the indexes, the allele map could be created for multiple collapsed records,
// some of which might be unused for this output line
int ir, j;
for (ir=0; ir<files->nreaders; ir++)
{
bcf1_t *line = maux_get_line(args,ir);
if ( !line ) continue;
for (j=1; j<line->n_allele; j++)
{
int irec = ma->buf[ir].cur;
if ( ma->buf[ir].rec[irec].map[j]==i ) ma->buf[ir].rec[irec].map[j] = ma->nout_als;
}
}
}
// Expand the arrays and realloc the alleles string. Note that all alleles are in a single allocated block.
ma->nout_als++;
hts_expand0(char*, ma->nout_als, ma->mout_als, ma->out_als);
int k = 0;
for (i=0; i<ma->nals; i++)
if ( i==0 || al_idxs[i] ) ma->out_als[k++] = strdup(ma->als[i]);
assert( k==ma->nout_als );
normalize_alleles(ma->out_als, ma->nout_als);
bcf_update_alleles(out_hdr, out, (const char**) ma->out_als, ma->nout_als);
free(al_idxs);
for (i=0; i<ma->nout_als; i++) free(ma->out_als[i]);
}
void merge_filter(args_t *args, bcf1_t *out)
{
bcf_srs_t *files = args->files;
bcf_hdr_t *out_hdr = args->out_hdr;
int i, ret;
if ( args->filter_logic == FLT_LOGIC_REMOVE )
{
for (i=0; i<files->nreaders; i++)
{
bcf1_t *line = maux_get_line(args, i);
if ( !line ) continue;
bcf_sr_t *reader = &files->readers[i];
bcf_hdr_t *hdr = reader->header;
if ( bcf_has_filter(hdr, line, "PASS") ) break;
}
if ( i<files->nreaders )
{
int flt_id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, "PASS");
bcf_add_filter(out_hdr, out, flt_id);
return;
}
}
khiter_t kitr;
strdict_t *tmph = args->tmph;
kh_clear(strdict, tmph);
out->d.n_flt = 0;
for (i=0; i<files->nreaders; i++)
{
bcf1_t *line = maux_get_line(args, i);
if ( !line ) continue;
bcf_sr_t *reader = &files->readers[i];
bcf_hdr_t *hdr = reader->header;
int k;
for (k=0; k<line->d.n_flt; k++)
{
const char *flt = hdr->id[BCF_DT_ID][line->d.flt[k]].key;
kitr = kh_get(strdict, tmph, flt);
if ( kitr == kh_end(tmph) )
{
int id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, flt);
if ( id==-1 ) error("Error: The filter is not defined in the header: %s\n", flt);
hts_expand(int,out->d.n_flt+1,out->d.m_flt,out->d.flt);
out->d.flt[out->d.n_flt] = id;
out->d.n_flt++;
kh_put(strdict, tmph, flt, &ret);
}
}
}
// Check if PASS is not mixed with other filters
if ( out->d.n_flt>1 )
{
int id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, "PASS");
for (i=0; i<out->d.n_flt; i++)
if ( out->d.flt[i]==id ) break;
if ( i<out->d.n_flt )
{
out->d.n_flt--;
for (; i<out->d.n_flt; i++) out->d.flt[i] = out->d.flt[i+1];
}
}
}
static void bcf_info_set_id(bcf1_t *line, bcf_info_t *info, int id, kstring_t *tmp_str)
{
uint8_t *ptr = info->vptr - info->vptr_off;
bcf_dec_typed_int1(ptr, &ptr);
tmp_str->l = 0;
bcf_enc_int1(tmp_str, id);
if ( tmp_str->l == ptr - info->vptr + info->vptr_off )
{
// the new id is represented with the same number of bytes
memcpy(info->vptr - info->vptr_off, tmp_str->s, tmp_str->l);
return;
}
kputsn_(ptr, info->vptr - ptr, tmp_str);
info->vptr_off = tmp_str->l;
kputsn_(info->vptr, info->len << bcf_type_shift[info->type], tmp_str);
info->vptr = (uint8_t*) tmp_str->s + info->vptr_off;
tmp_str->s = NULL;
tmp_str->m = 0;
tmp_str->l = 0;