static void init_data(args_t *args)
{
args->hdr = args->files->readers[0].header;
args->hdr_out = bcf_hdr_dup(args->hdr);
init_plugin(args);
if ( args->filter_str )
args->filter = filter_init(args->hdr, args->filter_str);
bcf_hdr_append_version(args->hdr_out, args->argc, args->argv, "bcftools_plugin");
if ( !args->drop_header )
{
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));
bcf_hdr_write(args->out_fh, args->hdr_out);
}
}
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);
}
int i;
if ( !bcf_sr_add_reader(args->aux.srs, args->bcf_fname) ) error("Failed to open: %s\n", args->bcf_fname);
if ( args->nsamples && args->nsamples != bcf_hdr_nsamples(args->aux.srs->readers[0].header) )
{
args->samples_map = (int *) malloc(sizeof(int)*args->nsamples);
args->aux.hdr = bcf_hdr_subset(args->aux.srs->readers[0].header, args->nsamples, args->samples, args->samples_map);
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(args->aux.srs->readers[0].header);
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]);
}
// Reorder ploidy and family indexes to match mpileup's output and exclude samples which are not available
if ( args->aux.ploidy )
{
for (i=0; i<args->aux.nfams; i++)
{
int j;
for (j=0; j<3; j++)
{
int k = bcf_hdr_id2int(args->aux.hdr, BCF_DT_SAMPLE, args->samples[ args->aux.fams[i].sample[j] ]);
if ( k<0 ) error("No such sample: %s\n", args->samples[ args->aux.fams[i].sample[j] ]);
args->aux.fams[i].sample[j] = k;
}
}
uint8_t *ploidy = (uint8_t*) calloc(bcf_hdr_nsamples(args->aux.hdr), 1);
for (i=0; i<args->nsamples; i++) // i index in -s sample list
{
int j = bcf_hdr_id2int(args->aux.hdr, BCF_DT_SAMPLE, args->samples[i]); // j index in the output VCF / subset VCF
if ( j<0 )
{
fprintf(stderr,"Warning: no such sample: \"%s\"\n", args->samples[i]);
continue;
}
ploidy[j] = args->aux.ploidy[i];
}
args->nsamples = bcf_hdr_nsamples(args->aux.hdr);
for (i=0; i<args->nsamples; i++)
assert( ploidy[i]==0 || ploidy[i]==1 || ploidy[i]==2 );
free(args->aux.ploidy);
args->aux.ploidy = ploidy;
}
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);
}
void isec_vcf(args_t *args)
{
bcf_srs_t *files = args->files;
kstring_t str = {0,0,0};
htsFile *out_fh = NULL;
// When only one VCF is output, print VCF to pysam_stdout or -o file
int out_std = 0;
if ( args->nwrite==1 && !args->prefix ) out_std = 1;
if ( args->targets_list && files->nreaders==1 ) out_std = 1;
if ( out_std )
{
out_fh = hts_open(args->output_fname? args->output_fname : "-",hts_bcf_wmode(args->output_type));
if ( out_fh == NULL ) error("Can't write to %s: %s\n", args->output_fname? args->output_fname : "standard output", strerror(errno));
if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
if (args->record_cmd_line) bcf_hdr_append_version(files->readers[args->iwrite].header,args->argc,args->argv,"bcftools_isec");
bcf_hdr_write(out_fh, files->readers[args->iwrite].header);
}
if ( !args->nwrite && !out_std && !args->prefix )
fprintf(pysam_stderr,"Note: -w option not given, printing list of sites...\n");
int n;
while ( (n=bcf_sr_next_line(files)) )
{
bcf_sr_t *reader = NULL;
bcf1_t *line = NULL;
int i, ret = 0;
for (i=0; i<files->nreaders; i++)
{
if ( !bcf_sr_has_line(files,i) ) continue;
if ( args->nflt && args->flt[i] )
{
bcf1_t *rec = bcf_sr_get_line(files, i);
int pass = filter_test(args->flt[i], rec, NULL);
if ( args->flt_logic[i] & FLT_EXCLUDE ) pass = pass ? 0 : 1;
if ( !pass )
{
files->has_line[i] = 0;
n--;
continue;
}
}
if ( !line )
{
line = files->readers[i].buffer[0];
reader = &files->readers[i];
}
ret |= 1<<i; // this may overflow for many files, but will be used only with two (OP_VENN)
}
switch (args->isec_op)
{
case OP_COMPLEMENT: if ( n!=1 || !bcf_sr_has_line(files,0) ) continue; break;
case OP_EQUAL: if ( n != args->isec_n ) continue; break;
case OP_PLUS: if ( n < args->isec_n ) continue; break;
case OP_MINUS: if ( n > args->isec_n ) continue; break;
case OP_EXACT:
for (i=0; i<files->nreaders; i++)
if ( files->has_line[i] != args->isec_exact[i] ) break;
if ( i<files->nreaders ) continue;
break;
}
if ( out_std )
{
if ( bcf_sr_has_line(files,args->iwrite) )
bcf_write1(out_fh, files->readers[args->iwrite].header, files->readers[args->iwrite].buffer[0]);
continue;
}
else if ( args->fh_sites )
{
str.l = 0;
kputs(reader->header->id[BCF_DT_CTG][line->rid].key, &str); kputc('\t', &str);
kputw(line->pos+1, &str); kputc('\t', &str);
if (line->n_allele > 0) kputs(line->d.allele[0], &str);
else kputc('.', &str);
kputc('\t', &str);
if (line->n_allele > 1) kputs(line->d.allele[1], &str);
else kputc('.', &str);
for (i=2; i<line->n_allele; i++)
{
kputc(',', &str);
kputs(line->d.allele[i], &str);
}
kputc('\t', &str);
for (i=0; i<files->nreaders; i++)
kputc(bcf_sr_has_line(files,i)?'1':'0', &str);
kputc('\n', &str);
fwrite(str.s,sizeof(char),str.l,args->fh_sites);
}
if ( args->prefix )
{
if ( args->isec_op==OP_VENN && ret==3 )
{
if ( !args->nwrite || args->write[0] )
bcf_write1(args->fh_out[2], bcf_sr_get_header(files,0), bcf_sr_get_line(files,0));
if ( !args->nwrite || args->write[1] )
bcf_write1(args->fh_out[3], bcf_sr_get_header(files,1), bcf_sr_get_line(files,1));
}
else
{
for (i=0; i<files->nreaders; i++)
{
if ( !bcf_sr_has_line(files,i) ) continue;
if ( args->write && !args->write[i] ) continue;
bcf_write1(args->fh_out[i], files->readers[i].header, files->readers[i].buffer[0]);
}
}
}
}
if ( str.s ) free(str.s);
if ( out_fh ) hts_close(out_fh);
}
static void init_data(args_t *args)
{
bcf1_t *line = NULL;
// With phased concat, the chunks overlap and come in the right order. To
// avoid opening all files at once, store start positions to recognise need
// for the next one. This way we can keep only two open chunks at once.
if ( args->phased_concat )
{
args->start_pos = (int*) malloc(sizeof(int)*args->nfnames);
line = bcf_init();
}
kstring_t str = {0,0,0};
int i, prev_chrid = -1;
for (i=0; i<args->nfnames; i++)
{
htsFile *fp = hts_open(args->fnames[i], "r"); if ( !fp ) error("Failed to open: %s\n", args->fnames[i]);
bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to parse header: %s\n", args->fnames[i]);
args->out_hdr = bcf_hdr_merge(args->out_hdr,hdr);
if ( bcf_hdr_nsamples(hdr) != bcf_hdr_nsamples(args->out_hdr) )
error("Different number of samples in %s. Perhaps \"bcftools merge\" is what you are looking for?\n", args->fnames[i]);
int j;
for (j=0; j<bcf_hdr_nsamples(hdr); j++)
if ( strcmp(args->out_hdr->samples[j],hdr->samples[j]) )
error("Different sample names in %s. Perhaps \"bcftools merge\" is what you are looking for?\n", args->fnames[i]);
if ( args->phased_concat )
{
int ret = bcf_read(fp, hdr, line);
if ( ret!=0 ) args->start_pos[i] = -2; // empty file
else
{
int chrid = bcf_hdr_id2int(args->out_hdr,BCF_DT_CTG,bcf_seqname(hdr,line));
args->start_pos[i] = chrid==prev_chrid ? line->pos : -1;
prev_chrid = chrid;
}
}
bcf_hdr_destroy(hdr);
hts_close(fp);
}
free(str.s);
if ( line ) bcf_destroy(line);
args->seen_seq = (int*) calloc(args->out_hdr->n[BCF_DT_CTG],sizeof(int));
if ( args->phased_concat )
{
bcf_hdr_append(args->out_hdr,"##FORMAT=<ID=PQ,Number=1,Type=Integer,Description=\"Phasing Quality (bigger is better)\">");
bcf_hdr_append(args->out_hdr,"##FORMAT=<ID=PS,Number=1,Type=Integer,Description=\"Phase Set\">");
}
if (args->record_cmd_line) bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_concat");
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->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
bcf_hdr_write(args->out_fh, args->out_hdr);
if ( args->allow_overlaps )
{
args->files = bcf_sr_init();
args->files->require_index = 1;
if ( args->regions_list )
{
if ( bcf_sr_set_regions(args->files, args->regions_list, args->regions_is_file)<0 )
error("Failed to read the regions: %s\n", args->regions_list);
}
if ( args->remove_dups )
{
if ( !strcmp(args->remove_dups,"snps") ) args->files->collapse |= COLLAPSE_SNPS;
else if ( !strcmp(args->remove_dups,"indels") ) args->files->collapse |= COLLAPSE_INDELS;
else if ( !strcmp(args->remove_dups,"both") ) args->files->collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS;
else if ( !strcmp(args->remove_dups,"any") ) args->files->collapse |= COLLAPSE_ANY;
else if ( !strcmp(args->remove_dups,"all") ) args->files->collapse |= COLLAPSE_ANY;
else if ( !strcmp(args->remove_dups,"none") ) args->files->collapse = COLLAPSE_NONE;
else error("The -D string \"%s\" not recognised.\n", args->remove_dups);
}
for (i=0; i<args->nfnames; i++)
if ( !bcf_sr_add_reader(args->files,args->fnames[i]) ) error("Failed to open %s: %s\n", args->fnames[i],bcf_sr_strerror(args->files->errnum));
}
else if ( args->phased_concat )
{
// Remove empty files from the list
int nok = 0;
while (1)
{
while ( nok<args->nfnames && args->start_pos[nok]!=-2 ) nok++;
if ( nok==args->nfnames ) break;
i = nok;
while ( i<args->nfnames && args->start_pos[i]==-2 ) i++;
if ( i==args->nfnames ) break;
int tmp = args->start_pos[nok]; args->start_pos[nok] = args->start_pos[i]; args->start_pos[i] = tmp;
char *str = args->fnames[nok]; args->fnames[nok] = args->fnames[i]; args->fnames[i] = str;
}
for (i=nok; i<args->nfnames; i++) free(args->fnames[i]);
args->nfnames = nok;
for (i=1; i<args->nfnames; i++)
if ( args->start_pos[i-1]!=-1 && args->start_pos[i]!=-1 && args->start_pos[i]<args->start_pos[i-1] )
error("The files not in ascending order: %d in %s, %d in %s\n", args->start_pos[i-1]+1,args->fnames[i-1],args->start_pos[i]+1,args->fnames[i]);
args->prev_chr = -1;
args->swap_phase = (int*) calloc(bcf_hdr_nsamples(args->out_hdr),sizeof(int));
args->nmatch = (int*) calloc(bcf_hdr_nsamples(args->out_hdr),sizeof(int));
args->nmism = (int*) calloc(bcf_hdr_nsamples(args->out_hdr),sizeof(int));
args->phase_qual = (int32_t*) malloc(bcf_hdr_nsamples(args->out_hdr)*sizeof(int32_t));
args->phase_set = (int32_t*) malloc(bcf_hdr_nsamples(args->out_hdr)*sizeof(int32_t));
args->files = bcf_sr_init();
args->files->require_index = 1;
args->ifname = 0;
}
}
void isec_vcf(args_t *args)
{
bcf_srs_t *files = args->files;
kstring_t str = {0,0,0};
htsFile *out_fh = NULL;
// When only one VCF is output, print VCF to stdout
int out_std = 0;
if ( args->nwrite==1 ) out_std = 1;
if ( args->targets_list && files->nreaders==1 ) out_std = 1;
if ( out_std )
{
out_fh = hts_open("-",hts_bcf_wmode(args->output_type));
bcf_hdr_append_version(files->readers[args->iwrite].header,args->argc,args->argv,"bcftools_isec");
bcf_hdr_write(out_fh, files->readers[args->iwrite].header);
}
if ( !args->nwrite && !out_std && !args->prefix )
fprintf(stderr,"Note: -w option not given, printing list of sites...\n");
int n;
while ( (n=bcf_sr_next_line(files)) )
{
bcf_sr_t *reader = NULL;
bcf1_t *line = NULL;
int i, ret = 0;
for (i=0; i<files->nreaders; i++)
{
if ( !bcf_sr_has_line(files,i) ) continue;
if ( !line )
{
line = files->readers[i].buffer[0];
reader = &files->readers[i];
}
ret |= 1<<i; // this may overflow for many files, but will be used only with two (OP_VENN)
}
switch (args->isec_op)
{
case OP_COMPLEMENT: if ( n!=1 || !bcf_sr_has_line(files,0) ) continue; break;
case OP_EQUAL: if ( n != args->isec_n ) continue; break;
case OP_PLUS: if ( n < args->isec_n ) continue; break;
case OP_MINUS: if ( n > args->isec_n ) continue;
}
if ( out_std )
{
if ( bcf_sr_has_line(files,args->iwrite) )
bcf_write1(out_fh, files->readers[args->iwrite].header, files->readers[args->iwrite].buffer[0]);
continue;
}
else if ( args->fh_sites )
{
str.l = 0;
kputs(reader->header->id[BCF_DT_CTG][line->rid].key, &str); kputc('\t', &str);
kputw(line->pos+1, &str); kputc('\t', &str);
if (line->n_allele > 0) kputs(line->d.allele[0], &str);
else kputc('.', &str);
kputc('\t', &str);
if (line->n_allele > 1) kputs(line->d.allele[1], &str);
else kputc('.', &str);
for (i=2; i<line->n_allele; i++)
{
kputc(',', &str);
kputs(line->d.allele[i], &str);
}
kputc('\t', &str);
for (i=0; i<files->nreaders; i++)
kputc(bcf_sr_has_line(files,i)?'1':'0', &str);
kputc('\n', &str);
fwrite(str.s,sizeof(char),str.l,args->fh_sites);
}
if ( args->prefix )
{
if ( args->isec_op==OP_VENN )
bcf_write1(args->fh_out[ret-1], reader->header, line);
else
{
for (i=0; i<files->nreaders; i++)
{
if ( !bcf_sr_has_line(files,i) ) continue;
if ( args->write && !args->write[i] ) continue;
bcf_write1(args->fh_out[i], files->readers[i].header, files->readers[i].buffer[0]);
}
}
}
}
if ( str.s ) free(str.s);
if ( out_fh ) hts_close(out_fh);
}
static void init_data(args_t *args)
{
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->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
args->hdr = args->files->readers[0].header;
args->flt_pass = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"PASS"); assert( !args->flt_pass ); // sanity check: required by BCF spec
// -i or -e: append FILTER line
if ( args->soft_filter && args->filter_logic )
{
kstring_t flt_name = {0,0,0};
if ( strcmp(args->soft_filter,"+") )
kputs(args->soft_filter, &flt_name);
else
{
// Make up a filter name
int i = 0, id = -1;
do
{
ksprintf(&flt_name,"Filter%d", ++i);
id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,flt_name.s);
}
while ( bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FLT,id) );
}
// escape quotes
kstring_t tmp = {0,0,0};
char *t = args->filter_str;
while ( *t )
{
if ( *t=='"' ) kputc('\\',&tmp);
kputc(*t,&tmp);
t++;
}
int ret = bcf_hdr_printf(args->hdr, "##FILTER=<ID=%s,Description=\"Set if %s: %s\">", flt_name.s,args->filter_logic & FLT_INCLUDE ? "not true" : "true", tmp.s);
if ( ret!=0 )
error("Failed to append header line: ##FILTER=<ID=%s,Description=\"Set if %s: %s\">\n", flt_name.s,args->filter_logic & FLT_INCLUDE ? "not true" : "true", tmp.s);
args->flt_fail = bcf_hdr_id2int(args->hdr,BCF_DT_ID,flt_name.s); assert( args->flt_fail>=0 );
free(flt_name.s);
free(tmp.s);
}
if ( args->snp_gap || args->indel_gap )
{
if ( !args->filter_logic && args->soft_filter && strcmp(args->soft_filter,"+") )
{
kstring_t tmp = {0,0,0};
if ( args->snp_gap ) kputs("\"SnpGap\"", &tmp);
if ( args->indel_gap )
{
if ( tmp.s ) kputs(" and ", &tmp);
kputs("\"IndelGap\"", &tmp);
}
fprintf(stderr,"Warning: using %s filter name instead of \"%s\"\n", tmp.s,args->soft_filter);
free(tmp.s);
}
rbuf_init(&args->rbuf, 64);
args->rbuf_lines = (bcf1_t**) calloc(args->rbuf.m, sizeof(bcf1_t*));
if ( args->snp_gap )
{
bcf_hdr_printf(args->hdr, "##FILTER=<ID=SnpGap,Description=\"SNP within %d bp of an indel\">", args->snp_gap);
args->SnpGap_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "SnpGap");
assert( args->SnpGap_id>=0 );
}
if ( args->indel_gap )
{
bcf_hdr_printf(args->hdr, "##FILTER=<ID=IndelGap,Description=\"Indel within %d bp of an indel\">", args->indel_gap);
args->IndelGap_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "IndelGap");
assert( args->IndelGap_id>=0 );
}
}
if (args->record_cmd_line) bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_filter");
if ( args->filter_str )
args->filter = filter_init(args->hdr, args->filter_str);
}
static void init_data(args_t *args)
{
int i;
args->hdr = args->files->readers[0].header;
if (args->calc_ac && args->update_info)
{
bcf_hdr_append(args->hdr,"##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes\">");
bcf_hdr_append(args->hdr,"##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">");
}
bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_view");
// setup sample data
if (args->sample_names)
{
void *hdr_samples = khash_str2int_init();
for (i=0; i<bcf_hdr_nsamples(args->hdr); i++)
khash_str2int_inc(hdr_samples, bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i));
void *exclude = (args->sample_names[0]=='^') ? khash_str2int_init() : NULL;
int nsmpl;
char **smpl = NULL;
args->samples = NULL; args->n_samples = 0;
smpl = hts_readlist(exclude ? &args->sample_names[1] : args->sample_names, args->sample_is_file, &nsmpl);
if ( !smpl )
{
error("Could not read the list: \"%s\"\n", exclude ? &args->sample_names[1] : args->sample_names);
}
if ( exclude )
{
for (i=0; i<nsmpl; i++) {
if (!khash_str2int_has_key(hdr_samples,smpl[i])) {
if (args->force_samples) {
fprintf(stderr, "Warn: exclude called for sample that does not exist in header: \"%s\"... skipping\n", smpl[i]);
} else {
error("Error: exclude called for sample that does not exist in header: \"%s\". Use \"--force-samples\" to ignore this error.\n", smpl[i]);
}
}
khash_str2int_inc(exclude, smpl[i]);
}
for (i=0; i<bcf_hdr_nsamples(args->hdr); i++)
{
if ( exclude && khash_str2int_has_key(exclude,bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i)) ) continue;
args->samples = (char**) realloc(args->samples, (args->n_samples+1)*sizeof(const char*));
args->samples[args->n_samples++] = strdup(bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i));
}
khash_str2int_destroy(exclude);
}
else
{
for (i=0; i<nsmpl; i++) {
if (!khash_str2int_has_key(hdr_samples,smpl[i])) {
if (args->force_samples) {
fprintf(stderr, "Warn: subset called for sample that does not exist in header: \"%s\"... skipping\n", smpl[i]);
continue;
} else {
error("Error: subset called for sample that does not exist in header: \"%s\". Use \"--force-samples\" to ignore this error.\n", smpl[i]);
}
}
args->samples = (char**) realloc(args->samples, (args->n_samples+1)*sizeof(const char*));
args->samples[args->n_samples++] = strdup(smpl[i]);
}
}
for (i=0; i<nsmpl; i++) free(smpl[i]);
free(smpl);
khash_str2int_destroy(hdr_samples);
if (args->n_samples == 0) {
fprintf(stderr, "Warn: subsetting has removed all samples\n");
args->sites_only = 1;
}
}
if (args->n_samples)
args->imap = (int*)malloc(args->n_samples * sizeof(int));
// determine variant types to include/exclude
if (args->include_types || args->exclude_types) {
if (args->include_types && args->exclude_types) {
fprintf(stderr, "Error: only supply one of --include-types, --exclude-types options\n");
exit(1);
}
char **type_list = 0;
int m = 0, n = 0;
const char *q, *p;
for (q = p = args->include_types ? args->include_types : args->exclude_types;; ++p) {
if (*p == ',' || *p == 0) {
if (m == n) {
m = m? m<<1 : 16;
type_list = (char**)realloc(type_list, m * sizeof(char*));
}
type_list[n] = (char*)calloc(p - q + 1, 1);
strncpy(type_list[n++], q, p - q);
q = p + 1;
if (*p == 0) break;
}
}
type_list = (char**)realloc(type_list, n * sizeof(char*));
if (args->include_types) {
args->include = 0;
for (i = 0; i < n; ++i) {
if (strcmp(type_list[i], "snps") == 0) args->include |= VCF_SNP;
else if (strcmp(type_list[i], "indels") == 0) args->include |= VCF_INDEL;
else if (strcmp(type_list[i], "mnps") == 0) args->include |= VCF_MNP;
else if (strcmp(type_list[i], "other") == 0) args->include |= VCF_OTHER;
else {
fprintf(stderr, "[E::%s] unknown type\n", type_list[i]);
fprintf(stderr, "Accepted types are snps, indels, mnps, other\n");
exit(1);
}
}
}
if (args->exclude_types) {
args->exclude = 0;
for (i = 0; i < n; ++i) {
if (strcmp(type_list[i], "snps") == 0) args->exclude |= VCF_SNP;
else if (strcmp(type_list[i], "indels") == 0) args->exclude |= VCF_INDEL;
else if (strcmp(type_list[i], "mnps") == 0) args->exclude |= VCF_MNP;
else if (strcmp(type_list[i], "other") == 0) args->exclude |= VCF_OTHER;
else {
fprintf(stderr, "[E::%s] unknown type\n", type_list[i]);
fprintf(stderr, "Accepted types are snps, indels, mnps, other\n");
exit(1);
}
}
}
for (i = 0; i < n; ++i)
free(type_list[i]);
free(type_list);
}
// setup output
char modew[8];
strcpy(modew, "w");
if (args->clevel >= 0 && args->clevel <= 9) sprintf(modew + 1, "%d", args->clevel);
if (args->output_type==FT_BCF) strcat(modew, "bu"); // uncompressed BCF
else if (args->output_type & FT_BCF) strcat(modew, "b"); // compressed BCF
else if (args->output_type & FT_GZ) strcat(modew,"z"); // compressed VCF
args->out = hts_open(args->fn_out ? args->fn_out : "-", modew);
if ( !args->out ) error("%s: %s\n", args->fn_out,strerror(errno));
// headers: hdr=full header, hsub=subset header, hnull=sites only header
if (args->sites_only){
args->hnull = bcf_hdr_subset(args->hdr, 0, 0, 0);
bcf_hdr_remove(args->hnull, BCF_HL_FMT, NULL);
}
if (args->n_samples > 0)
{
args->hsub = bcf_hdr_subset(args->hdr, args->n_samples, args->samples, args->imap);
if ( !args->hsub ) error("Error occurred while subsetting samples\n");
if ( args->n_samples != bcf_hdr_nsamples(args->hsub) )
{
int i;
for (i=0; i<args->n_samples; i++)
if ( args->imap[i]<0 ) error("Error: No such sample: \"%s\"\n", args->samples[i]);
}
}
if ( args->filter_str )
args->filter = filter_init(args->hdr, args->filter_str);
}
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);
}
