int main_vcfisec(int argc, char *argv[])
{
int c;
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->files = bcf_sr_init();
args->argc = argc; args->argv = argv;
args->output_fname = NULL;
args->output_type = FT_VCF;
args->n_threads = 0;
args->record_cmd_line = 1;
int targets_is_file = 0, regions_is_file = 0;
static struct option loptions[] =
{
{"help",no_argument,NULL,'h'},
{"exclude",required_argument,NULL,'e'},
{"include",required_argument,NULL,'i'},
{"collapse",required_argument,NULL,'c'},
{"complement",no_argument,NULL,'C'},
{"apply-filters",required_argument,NULL,'f'},
{"nfiles",required_argument,NULL,'n'},
{"prefix",required_argument,NULL,'p'},
{"write",required_argument,NULL,'w'},
{"targets",required_argument,NULL,'t'},
{"targets-file",required_argument,NULL,'T'},
{"regions",required_argument,NULL,'r'},
{"regions-file",required_argument,NULL,'R'},
{"output",required_argument,NULL,'o'},
{"output-type",required_argument,NULL,'O'},
{"threads",required_argument,NULL,9},
{"no-version",no_argument,NULL,8},
{NULL,0,NULL,0}
};
while ((c = getopt_long(argc, argv, "hc:r:R:p:n:w:t:T:Cf:o:O:i:e:",loptions,NULL)) >= 0) {
switch (c) {
case 'o': args->output_fname = optarg; break;
case 'O':
switch (optarg[0]) {
case 'b': args->output_type = FT_BCF_GZ; break;
case 'u': args->output_type = FT_BCF; break;
case 'z': args->output_type = FT_VCF_GZ; break;
case 'v': args->output_type = FT_VCF; break;
default: error("The output type \"%s\" not recognised\n", optarg);
}
break;
case 'c':
if ( !strcmp(optarg,"snps") ) args->files->collapse |= COLLAPSE_SNPS;
else if ( !strcmp(optarg,"indels") ) args->files->collapse |= COLLAPSE_INDELS;
else if ( !strcmp(optarg,"both") ) args->files->collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS;
else if ( !strcmp(optarg,"any") ) args->files->collapse |= COLLAPSE_ANY;
else if ( !strcmp(optarg,"all") ) args->files->collapse |= COLLAPSE_ANY;
else if ( !strcmp(optarg,"some") ) args->files->collapse |= COLLAPSE_SOME;
else if ( !strcmp(optarg,"none") ) args->files->collapse = COLLAPSE_NONE;
else error("The --collapse string \"%s\" not recognised.\n", optarg);
break;
case 'f': args->files->apply_filters = optarg; break;
case 'C': args->isec_op = OP_COMPLEMENT; break;
case 'r': args->regions_list = optarg; break;
case 'R': args->regions_list = optarg; regions_is_file = 1; break;
case 't': args->targets_list = optarg; break;
case 'T': args->targets_list = optarg; targets_is_file = 1; break;
case 'p': args->prefix = optarg; break;
case 'w': args->write_files = optarg; break;
case 'i': add_filter(args, optarg, FLT_INCLUDE); break;
case 'e': add_filter(args, optarg, FLT_EXCLUDE); break;
case 'n':
{
char *p = optarg;
if ( *p=='-' ) { args->isec_op = OP_MINUS; p++; }
else if ( *p=='+' ) { args->isec_op = OP_PLUS; p++; }
else if ( *p=='=' ) { args->isec_op = OP_EQUAL; p++; }
else if ( *p=='~' ) { args->isec_op = OP_EXACT; p++; }
else if ( isdigit(*p) ) args->isec_op = OP_EQUAL;
else error("Could not parse --nfiles %s\n", optarg);
if ( args->isec_op == OP_EXACT ) args->isec_exact = p;
else if ( sscanf(p,"%d",&args->isec_n)!=1 ) error("Could not parse --nfiles %s\n", optarg);
}
break;
case 9 : args->n_threads = strtol(optarg, 0, 0); break;
case 8 : args->record_cmd_line = 0; break;
case 'h':
case '?': usage();
default: error("Unknown argument: %s\n", optarg);
}
}
if ( argc-optind<1 ) usage(); // no file given
if ( args->targets_list && bcf_sr_set_targets(args->files, args->targets_list, targets_is_file,0)<0 )
error("Failed to read the targets: %s\n", args->targets_list);
if ( args->regions_list && bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
error("Failed to read the regions: %s\n", args->regions_list);
if ( argc-optind==2 && !args->isec_op )
{
args->isec_op = OP_VENN;
if ( !args->prefix ) error("Expected the -p option\n");
}
if ( !args->targets_list )
{
if ( argc-optind<2 ) error("Expected multiple files or the --targets option\n");
if ( !args->isec_op ) error("Expected two file names or one of the options --complement, --nfiles or --targets\n");
}
args->files->require_index = 1;
while (optind<argc)
{
if ( !bcf_sr_add_reader(args->files, argv[optind]) ) error("Failed to open %s: %s\n", argv[optind],bcf_sr_strerror(args->files->errnum));
optind++;
}
init_data(args);
isec_vcf(args);
destroy_data(args);
bcf_sr_destroy(args->files);
free(args);
return 0;
}
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;
}
}
static void init_data(args_t *args)
{
bcf_srs_t *files = bcf_sr_init();
if ( args->regions_list )
{
if ( bcf_sr_set_regions(files, args->regions_list, args->regions_is_file)<0 )
error("Failed to read the regions: %s\n", args->regions_list);
}
if ( args->targets_list )
{
if ( bcf_sr_set_targets(files, args->targets_list, args->targets_is_file, 0)<0 )
error("Failed to read the targets: %s\n", args->targets_list);
}
if ( !bcf_sr_add_reader(files, args->fname) ) error("Failed to open %s: %s\n", args->fname,bcf_sr_strerror(files->errnum));
bcf_hdr_t *hdr = files->readers[0].header;
if ( !args->sample )
{
if ( bcf_hdr_nsamples(hdr)>1 ) error("Missing the option -s, --sample\n");
args->sample = hdr->samples[0];
}
else if ( bcf_hdr_id2int(hdr,BCF_DT_SAMPLE,args->sample)<0 ) error("No such sample: %s\n", args->sample);
int ret = bcf_hdr_set_samples(hdr, args->sample, 0);
if ( ret<0 ) error("Error setting the sample: %s\n", args->sample);
if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,bcf_hdr_id2int(hdr,BCF_DT_ID,"BAF")) )
error("The tag FORMAT/BAF is not present in the VCF: %s\n", args->fname);
int i;
args->xvals = (double*) calloc(args->nbins,sizeof(double));
for (i=0; i<args->nbins; i++) args->xvals[i] = 1.0*i/(args->nbins-1);
// collect BAF distributions for all chromosomes
int idist = -1, nbaf = 0, nprocessed = 0, ntotal = 0, prev_chr = -1;
float *baf = NULL;
while ( bcf_sr_next_line(files) )
{
ntotal++;
bcf1_t *line = bcf_sr_get_line(files,0);
if ( bcf_get_format_float(hdr,line,"BAF",&baf,&nbaf) != 1 ) continue;
if ( bcf_float_is_missing(baf[0]) ) continue;
nprocessed++;
if ( prev_chr==-1 || prev_chr!=line->rid )
{
// new chromosome
idist = args->ndist++;
args->dist = (dist_t*) realloc(args->dist, sizeof(dist_t)*args->ndist);
memset(&args->dist[idist],0,sizeof(dist_t));
args->dist[idist].chr = strdup(bcf_seqname(hdr,line));
args->dist[idist].yvals = (double*) calloc(args->nbins,sizeof(double));
args->dist[idist].xvals = args->xvals;
args->dist[idist].nvals = args->nbins;
prev_chr = line->rid;
}
int bin = baf[0]*(args->nbins-1);
args->dist[idist].yvals[bin]++; // the distribution
}
free(baf);
bcf_sr_destroy(files);
for (idist=0; idist<args->ndist; idist++)
{
#if 0
int j;
for (j=0; j<args->nbins; j++)
{
double x = args->dist[idist].xvals[j];
args->dist[idist].yvals[j] = exp(-(x-0.5)*(x-0.5)/1e-3);
}
#endif
init_dist(args, &args->dist[idist],args->verbose);
}
args->dat_fp = open_file(&args->dat_fname,"w","%s/dist.dat", args->output_dir);
fprintf(args->dat_fp, "# This file was produced by: bcftools polysomy(%s+htslib-%s), the command line was:\n", bcftools_version(),hts_version());
fprintf(args->dat_fp, "# \t bcftools %s ", args->argv[0]);
for (i=1; i<args->argc; i++)
fprintf(args->dat_fp, " %s",args->argv[i]);
fprintf(args->dat_fp,"\n#\n");
fprintf(args->dat_fp,"# DIST\t[2]Chrom\t[3]BAF\t[4]Normalized Count\n");
fprintf(args->dat_fp,"# FIT\t[2]Goodness of Fit\t[3]iFrom\t[4]iTo\t[5]The Fitted Function\n");
fprintf(args->dat_fp,"# CN\t[2]Chrom\t[3]Estimated Copy Number\t[4]Absolute fit deviation\n");
char *fname = NULL;
FILE *fp = open_file(&fname,"w","%s/dist.py", args->output_dir);
//-------- matplotlib script --------------
fprintf(fp,
"#!/usr/bin/env python\n"
"#\n"
"import matplotlib as mpl\n"
"mpl.use('Agg')\n"
"import matplotlib.pyplot as plt\n"
"import csv,sys,argparse\n"
"from math import exp\n"
"\n"
"outdir = '%s'\n"
"\n"
"def read_dat(dat,fit,cn):\n"
" csv.register_dialect('tab', delimiter='\t', quoting=csv.QUOTE_NONE)\n"
" with open(outdir+'/dist.dat', 'rb') as f:\n"
" reader = csv.reader(f, 'tab')\n"
" for row in reader:\n"
" if row[0][0]=='#': continue\n"
" type = row[0]\n"
" chr = row[1]\n"
" if type=='DIST':\n"
" if chr not in dat: dat[chr] = []\n"
" dat[chr].append(row)\n"
" elif type=='FIT':\n"
" if chr not in fit: fit[chr] = []\n"
" fit[chr].append(row)\n"
" elif type=='CN':\n"
" cn[chr] = row[2]\n"
"\n"
"def plot_dist(dat,fit,chr):\n"
" fig, ax = plt.subplots(1, 1, figsize=(7,5))\n"
" ax.plot([x[2] for x in dat[chr]],[x[3] for x in dat[chr]],'k-',label='Distribution')\n"
" if chr in fit:\n"
" for i in range(len(fit[chr])):\n"
" pfit = fit[chr][i]\n"
" exec('def xfit(x): return '+pfit[5])\n"
" istart = int(pfit[3])\n"
" iend = int(pfit[4])+1\n"
" vals = dat[chr][istart:iend]\n"
" args = {}\n"
" if i==0: args = {'label':'Target to Fit'}\n"
" ax.plot([x[2] for x in vals],[x[3] for x in vals],'r-',**args)\n"
" if i==0: args = {'label':'Best Fit'}\n"
" ax.plot([x[2] for x in vals],[xfit(float(x[2])) for x in vals],'g-',**args)\n"
" ax.set_title('BAF distribution, chr'+chr)\n"
" ax.set_xlabel('BAF')\n"
" ax.set_ylabel('Frequency')\n"
" ax.legend(loc='best',prop={'size':7},frameon=False)\n"
" plt.savefig(outdir+'/dist.chr'+chr+'.png')\n"
" plt.close()\n"
"\n"
"def plot_copy_number(cn):\n"
" fig, ax = plt.subplots(1, 1, figsize=(7,5))\n"
" xlabels = sorted(cn.keys())\n"
" xvals = range(len(xlabels))\n"
" yvals = [float(cn[x]) for x in xlabels]\n"
" ax.plot(xvals,yvals,'o',color='red')\n"
" for i in range(len(xvals)):\n"
" if yvals[i]==-1: ax.annotate('?', xy=(xvals[i],0.5),va='center',ha='center',color='red',fontweight='bold')\n"
" ax.tick_params(axis='both', which='major', labelsize=9)\n"
" ax.set_xticks(xvals)\n"
" ax.set_xticklabels(xlabels,rotation=45)\n"
" ax.set_xlim(-1,len(xlabels))\n"
" ax.set_ylim(0,5.0)\n"
" ax.set_yticks([1.0,2.0,3.0,4.0])\n"
" ax.set_xlabel('Chromosome')\n"
" ax.set_ylabel('Copy Number')\n"
" plt.savefig(outdir+'/copy-number.png')\n"
" plt.close()\n"
"\n"
"class myParser(argparse.ArgumentParser):\n"
" def error(self, message):\n"
" self.print_help()\n"
" sys.stderr.write('error: %%s\\n' %% message)\n"
" sys.exit(2)\n"
"\n"
"def main():\n"
" parser = myParser()\n"
" parser.add_argument('-a', '--all', action='store_true', help='Create all plots')\n"
" parser.add_argument('-c', '--copy-number', action='store_true', help='Create copy-number plot')\n"
" parser.add_argument('-d', '--distrib', metavar='CHR', help='Plot BAF distribution of a single chromosome')\n"
" args = parser.parse_args()\n"
" dat = {}; fit = {}; cn = {}\n"
" read_dat(dat,fit,cn)\n"
" if args.distrib!=None:\n"
" plot_dist(dat,fit,args.distrib)\n"
" if args.all:\n"
" for chr in dat: plot_dist(dat,fit,chr)\n"
" plot_copy_number(cn)\n"
" elif args.copy_number:\n"
" plot_copy_number(cn)\n"
" else:\n"
" for chr in dat: plot_dist(dat,fit,chr)\n"
"\n"
"if __name__ == '__main__':\n"
" main()\n",
args->output_dir);
//---------------------------------------
chmod(fname, S_IWUSR|S_IRUSR|S_IRGRP|S_IROTH|S_IXUSR|S_IXGRP|S_IXOTH);
free(fname);
fclose(fp);
}
static void init_data(args_t *args)
{
args->sr = bcf_sr_init();
if ( args->region )
{
args->sr->require_index = 1;
if ( bcf_sr_set_regions(args->sr, args->region, args->region_is_file)<0 ) error("Failed to read the regions: %s\n",args->region);
}
if ( args->target && bcf_sr_set_targets(args->sr, args->target, args->target_is_file, 0)<0 ) error("Failed to read the targets: %s\n",args->target);
if ( !bcf_sr_add_reader(args->sr,args->fname) ) error("Error: %s\n", bcf_sr_strerror(args->sr->errnum));
args->hdr_in = bcf_sr_get_header(args->sr,0);
args->hdr_out = bcf_hdr_dup(args->hdr_in);
if ( args->filter_str )
args->filter = filter_init(args->hdr_in, args->filter_str);
mkdir_p("%s/",args->output_dir);
int i, nsmpl = bcf_hdr_nsamples(args->hdr_in);
if ( !nsmpl ) error("No samples to split: %s\n", args->fname);
args->fh = (htsFile**)calloc(nsmpl,sizeof(*args->fh));
args->bnames = set_file_base_names(args);
kstring_t str = {0,0,0};
for (i=0; i<nsmpl; i++)
{
if ( !args->bnames[i] ) continue;
str.l = 0;
kputs(args->output_dir, &str);
if ( str.s[str.l-1] != '/' ) kputc('/', &str);
int k, l = str.l;
kputs(args->bnames[i], &str);
for (k=l; k<str.l; k++) if ( isspace(str.s[k]) ) str.s[k] = '_';
if ( args->output_type & FT_BCF ) kputs(".bcf", &str);
else if ( args->output_type & FT_GZ ) kputs(".vcf.gz", &str);
else kputs(".vcf", &str);
args->fh[i] = hts_open(str.s, hts_bcf_wmode(args->output_type));
if ( args->fh[i] == NULL ) error("Can't write to \"%s\": %s\n", str.s, strerror(errno));
bcf_hdr_nsamples(args->hdr_out) = 1;
args->hdr_out->samples[0] = args->bnames[i];
bcf_hdr_write(args->fh[i], args->hdr_out);
}
free(str.s);
// parse tags
int is_info = 0, is_fmt = 0;
char *beg = args->keep_tags;
while ( beg && *beg )
{
if ( !strncasecmp("INFO/",beg,5) ) { is_info = 1; is_fmt = 0; beg += 5; }
else if ( !strcasecmp("INFO",beg) ) { args->keep_info = 1; break; }
else if ( !strncasecmp("INFO,",beg,5) ) { args->keep_info = 1; beg += 5; continue; }
else if ( !strncasecmp("FMT/",beg,4) ) { is_info = 0; is_fmt = 1; beg += 4; }
else if ( !strncasecmp("FORMAT/",beg,7) ) { is_info = 0; is_fmt = 1; beg += 7; }
else if ( !strcasecmp("FMT",beg) ) { args->keep_fmt = 1; break; }
else if ( !strcasecmp("FORMAT",beg) ) { args->keep_fmt = 1; break; }
else if ( !strncasecmp("FMT,",beg,4) ) { args->keep_fmt = 1; beg += 4; continue; }
else if ( !strncasecmp("FORMAT,",beg,7) ) { args->keep_fmt = 1; beg += 7; continue; }
char *end = beg;
while ( *end && *end!=',' ) end++;
char tmp = *end; *end = 0;
int id = bcf_hdr_id2int(args->hdr_in, BCF_DT_ID, beg);
beg = tmp ? end + 1 : end;
if ( is_info && bcf_hdr_idinfo_exists(args->hdr_in,BCF_HL_INFO,id) )
{
if ( id >= args->ninfo_tags ) args->ninfo_tags = id + 1;
hts_expand0(uint8_t, args->ninfo_tags, args->minfo_tags, args->info_tags);
args->info_tags[id] = 1;
}
if ( is_fmt && bcf_hdr_idinfo_exists(args->hdr_in,BCF_HL_FMT,id) )
{
if ( id >= args->nfmt_tags ) args->nfmt_tags = id + 1;
hts_expand0(uint8_t, args->nfmt_tags, args->mfmt_tags, args->fmt_tags);
args->fmt_tags[id] = 1;
}
}
if ( !args->keep_info && !args->keep_fmt && !args->ninfo_tags && !args->nfmt_tags )
{
args->keep_info = args->keep_fmt = 1;
}
}
static void concat(args_t *args)
{
int i;
if ( args->phased_concat ) // phased concat
{
// keep only two open files at a time
while ( args->ifname < args->nfnames )
{
int new_file = 0;
while ( args->files->nreaders < 2 && args->ifname < args->nfnames )
{
if ( !bcf_sr_add_reader(args->files,args->fnames[args->ifname]) ) error("Failed to open %s: %s\n", args->fnames[args->ifname],bcf_sr_strerror(args->files->errnum));
new_file = 1;
args->ifname++;
if ( args->start_pos[args->ifname-1]==-1 ) break; // new chromosome, start with only one file open
if ( args->ifname < args->nfnames && args->start_pos[args->ifname]==-1 ) break; // next file starts on a different chromosome
}
// is there a line from the previous run? Seek the newly opened reader to that position
int seek_pos = -1;
int seek_chr = -1;
if ( bcf_sr_has_line(args->files,0) )
{
bcf1_t *line = bcf_sr_get_line(args->files,0);
bcf_sr_seek(args->files, bcf_seqname(args->files->readers[0].header,line), line->pos);
seek_pos = line->pos;
seek_chr = bcf_hdr_name2id(args->out_hdr, bcf_seqname(args->files->readers[0].header,line));
}
else if ( new_file )
bcf_sr_seek(args->files,NULL,0); // set to start
int nret;
while ( (nret = bcf_sr_next_line(args->files)) )
{
if ( !bcf_sr_has_line(args->files,0) ) // no input from the first reader
{
// We are assuming that there is a perfect overlap, sites which are not present in both files are dropped
if ( ! bcf_sr_region_done(args->files,0) ) continue;
phased_flush(args);
bcf_sr_remove_reader(args->files, 0);
}
// Get a line to learn about current position
for (i=0; i<args->files->nreaders; i++)
if ( bcf_sr_has_line(args->files,i) ) break;
bcf1_t *line = bcf_sr_get_line(args->files,i);
// This can happen after bcf_sr_seek: indel may start before the coordinate which we seek to.
if ( seek_chr>=0 && seek_pos>line->pos && seek_chr==bcf_hdr_name2id(args->out_hdr, bcf_seqname(args->files->readers[i].header,line)) ) continue;
seek_pos = seek_chr = -1;
// Check if the position overlaps with the next, yet unopened, reader
int must_seek = 0;
while ( args->ifname < args->nfnames && args->start_pos[args->ifname]!=-1 && line->pos >= args->start_pos[args->ifname] )
{
must_seek = 1;
if ( !bcf_sr_add_reader(args->files,args->fnames[args->ifname]) ) error("Failed to open %s: %s\n", args->fnames[args->ifname],bcf_sr_strerror(args->files->errnum));
args->ifname++;
}
if ( must_seek )
{
bcf_sr_seek(args->files, bcf_seqname(args->files->readers[i].header,line), line->pos);
seek_pos = line->pos;
seek_chr = bcf_hdr_name2id(args->out_hdr, bcf_seqname(args->files->readers[i].header,line));
continue;
}
// We are assuming that there is a perfect overlap, sites which are not present in both files are dropped
if ( args->files->nreaders>1 && !bcf_sr_has_line(args->files,1) && !bcf_sr_region_done(args->files,1) ) continue;
phased_push(args, bcf_sr_get_line(args->files,0), args->files->nreaders>1 ? bcf_sr_get_line(args->files,1) : NULL);
}
if ( args->files->nreaders )
{
phased_flush(args);
while ( args->files->nreaders )
bcf_sr_remove_reader(args->files, 0);
}
}
}
else if ( args->files ) // combining overlapping files, using synced reader
{
while ( bcf_sr_next_line(args->files) )
{
for (i=0; i<args->files->nreaders; i++)
{
bcf1_t *line = bcf_sr_get_line(args->files,i);
if ( !line ) continue;
bcf_translate(args->out_hdr, args->files->readers[i].header, line);
bcf_write1(args->out_fh, args->out_hdr, line);
if ( args->remove_dups ) break;
}
}
}
else // concatenating
{
kstring_t tmp = {0,0,0};
int prev_chr_id = -1, prev_pos;
bcf1_t *line = bcf_init();
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]);
if ( !fp->is_bin && args->output_type&FT_VCF )
{
line->max_unpack = BCF_UN_STR;
// if VCF is on both input and output, avoid VCF to BCF conversion
while ( hts_getline(fp, KS_SEP_LINE, &fp->line) >=0 )
{
char *str = fp->line.s;
while ( *str && *str!='\t' ) str++;
tmp.l = 0;
kputsn(fp->line.s,str-fp->line.s,&tmp);
int chr_id = bcf_hdr_name2id(args->out_hdr, tmp.s);
if ( chr_id<0 ) error("The sequence \"%s\" not defined in the header: %s\n(Quick workaround: index the file.)\n", tmp.s, args->fnames[i]);
if ( prev_chr_id!=chr_id )
{
prev_pos = -1;
if ( args->seen_seq[chr_id] )
error("\nThe chromosome block %s is not contiguous, consider running with -a.\n", tmp.s);
}
char *end;
int pos = strtol(str+1,&end,10) - 1;
if ( end==str+1 ) error("Could not parse line: %s\n", fp->line.s);
if ( prev_pos > pos )
error("The chromosome block %s is not sorted, consider running with -a.\n", tmp.s);
args->seen_seq[chr_id] = 1;
prev_chr_id = chr_id;
if ( vcf_write_line(args->out_fh, &fp->line)!=0 ) error("Failed to write %d bytes\n", fp->line.l);
}
}
else
{
// BCF conversion is required
line->max_unpack = 0;
while ( bcf_read(fp, hdr, line)==0 )
{
bcf_translate(args->out_hdr, hdr, line);
if ( prev_chr_id!=line->rid )
{
prev_pos = -1;
if ( args->seen_seq[line->rid] )
error("\nThe chromosome block %s is not contiguous, consider running with -a.\n", bcf_seqname(args->out_hdr, line));
}
if ( prev_pos > line->pos )
error("The chromosome block %s is not sorted, consider running with -a.\n", bcf_seqname(args->out_hdr, line));
args->seen_seq[line->rid] = 1;
prev_chr_id = line->rid;
if ( bcf_write(args->out_fh, args->out_hdr, line)!=0 ) error("Failed to write\n");
}
}
bcf_hdr_destroy(hdr);
hts_close(fp);
}
bcf_destroy(line);
free(tmp.s);
}
}
int main_vcfgtcheck(int argc, char *argv[])
{
int c;
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->files = bcf_sr_init();
args->argc = argc; args->argv = argv; set_cwd(args);
char *regions = NULL, *targets = NULL;
int regions_is_file = 0, targets_is_file = 0;
static struct option loptions[] =
{
{"GTs-only",1,0,'G'},
{"all-sites",0,0,'a'},
{"homs-only",0,0,'H'},
{"help",0,0,'h'},
{"genotypes",1,0,'g'},
{"plot",1,0,'p'},
{"target-sample",1,0,'S'},
{"query-sample",1,0,'s'},
{"regions",1,0,'r'},
{"regions-file",1,0,'R'},
{"targets",1,0,'t'},
{"targets-file",1,0,'T'},
{0,0,0,0}
};
char *tmp;
while ((c = getopt_long(argc, argv, "hg:p:s:S:Hr:R:at:T:G:",loptions,NULL)) >= 0) {
switch (c) {
case 'G':
args->no_PLs = strtol(optarg,&tmp,10);
if ( *tmp ) error("Could not parse argument: --GTs-only %s\n", optarg);
break;
case 'a': args->all_sites = 1; break;
case 'H': args->hom_only = 1; break;
case 'g': args->gt_fname = optarg; break;
case 'p': args->plot = optarg; break;
case 'S': args->target_sample = optarg; break;
case 's': args->query_sample = optarg; break;
case 'r': regions = optarg; break;
case 'R': regions = optarg; regions_is_file = 1; break;
case 't': targets = optarg; break;
case 'T': targets = optarg; targets_is_file = 1; break;
case 'h':
case '?': usage();
default: error("Unknown argument: %s\n", optarg);
}
}
char *fname = NULL;
if ( optind==argc )
{
if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin
else usage(); // no files given
}
else fname = argv[optind];
if ( argc>optind+1 ) usage(); // too many files given
if ( !args->gt_fname ) args->cross_check = 1; // no genotype file, run in cross-check mode
else args->files->require_index = 1;
if ( regions && bcf_sr_set_regions(args->files, regions, regions_is_file)<0 ) error("Failed to read the regions: %s\n", regions);
if ( targets && bcf_sr_set_targets(args->files, targets, targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", targets);
if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
if ( args->gt_fname && !bcf_sr_add_reader(args->files, args->gt_fname) ) error("Failed to open %s: %s\n", args->gt_fname,bcf_sr_strerror(args->files->errnum));
args->files->collapse = COLLAPSE_SNPS|COLLAPSE_INDELS;
if ( args->plot ) args->plot = init_prefix(args->plot);
init_data(args);
if ( args->cross_check )
cross_check_gts(args);
else
check_gt(args);
destroy_data(args);
bcf_sr_destroy(args->files);
if (args->plot) free(args->plot);
free(args);
return 0;
}
static void init_data(args_t *args)
{
args->files = bcf_sr_init();
args->files->require_index = 1;
if ( !bcf_sr_add_reader(args->files,args->fname) ) error("Failed to open %s: %s\n", args->fname, bcf_sr_strerror(args->files->errnum));
args->hdr = args->files->readers[0].header;
args->isample = -1;
if ( args->sample )
{
args->isample = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->sample);
if ( args->isample<0 ) error("No such sample: %s\n", args->sample);
}
if ( args->haplotype && args->isample<0 )
{
if ( bcf_hdr_nsamples(args->hdr) > 1 ) error("The --sample option is expected with --haplotype\n");
args->isample = 0;
}
if ( args->mask_fname )
{
args->mask = regidx_init(args->mask_fname,NULL,NULL,0,NULL);
if ( !args->mask ) error("Failed to initialize mask regions\n");
}
// In case we want to store the chains
if ( args->chain_fname )
{
args->fp_chain = fopen(args->chain_fname,"w");
if ( ! args->fp_chain ) error("Failed to create %s: %s\n", args->chain_fname, strerror(errno));
args->chain_id = 0;
}
rbuf_init(&args->vcf_rbuf, 100);
args->vcf_buf = (bcf1_t**) calloc(args->vcf_rbuf.m, sizeof(bcf1_t*));
if ( args->output_fname ) {
args->fp_out = fopen(args->output_fname,"w");
if ( ! args->fp_out ) error("Failed to create %s: %s\n", args->output_fname, strerror(errno));
}
else args->fp_out = stdout;
}
int main_plugin(int argc, char *argv[])
{
int c;
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->argc = argc;
args->argv = argv;
args->output_fname = "-";
args->output_type = FT_VCF;
args->nplugin_paths = -1;
int regions_is_file = 0, targets_is_file = 0, plist_only = 0, usage_only = 0, version_only = 0;
if ( argc==1 ) usage(args);
char *plugin_name = NULL;
if ( argv[1][0]!='-' ) {
plugin_name = argv[1];
argc--;
argv++;
}
static struct option loptions[] =
{
{"version",0,0,'V'},
{"verbose",0,0,'v'},
{"help",0,0,'h'},
{"list-plugins",0,0,'l'},
{"output",1,0,'o'},
{"output-type",1,0,'O'},
{"include",1,0,'i'},
{"exclude",1,0,'e'},
{"regions",1,0,'r'},
{"regions-file",1,0,'R'},
{"targets",1,0,'t'},
{"targets-file",1,0,'T'},
{0,0,0,0}
};
while ((c = getopt_long(argc, argv, "h?o:O:r:R:t:T:li:e:vV",loptions,NULL)) >= 0)
{
switch (c) {
case 'V':
version_only = 1;
break;
case 'v':
args->verbose = 1;
break;
case 'o':
args->output_fname = optarg;
break;
case 'O':
switch (optarg[0]) {
case 'b':
args->output_type = FT_BCF_GZ;
break;
case 'u':
args->output_type = FT_BCF;
break;
case 'z':
args->output_type = FT_VCF_GZ;
break;
case 'v':
args->output_type = FT_VCF;
break;
default:
error("The output type \"%s\" not recognised\n", optarg);
};
break;
case 'e':
args->filter_str = optarg;
args->filter_logic |= FLT_EXCLUDE;
break;
case 'i':
args->filter_str = optarg;
args->filter_logic |= FLT_INCLUDE;
break;
case 'r':
args->regions_list = optarg;
break;
case 'R':
args->regions_list = optarg;
regions_is_file = 1;
break;
case 't':
args->targets_list = optarg;
break;
case 'T':
args->targets_list = optarg;
targets_is_file = 1;
break;
case 'l':
plist_only = 1;
break;
case '?':
case 'h':
usage_only = 1;
break;
default:
error("Unknown argument: %s\n", optarg);
}
}
if ( plist_only ) return list_plugins(args);
if ( usage_only && ! plugin_name ) usage(args);
load_plugin(args, plugin_name, 1, &args->plugin);
if ( version_only )
{
const char *bver, *hver;
args->plugin.version(&bver, &hver);
printf("bcftools %s using htslib %s\n", bcftools_version(), hts_version());
printf("plugin at %s using htslib %s\n\n", bver, hver);
return 0;
}
if ( usage_only )
{
if ( args->plugin.usage )
fprintf(stderr,"%s",args->plugin.usage());
else
fprintf(stderr,"Usage: bcftools +%s [General Options] -- [Plugin Options]\n",plugin_name);
return 0;
}
if ( args->plugin.run )
{
int iopt = optind;
optind = 0;
int ret = args->plugin.run(argc-iopt, argv+iopt);
destroy_data(args);
free(args);
return ret;
}
char *fname = NULL;
if ( optind>=argc || argv[optind][0]=='-' )
{
if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin
else usage(args);
args->plugin.argc = argc - optind + 1;
args->plugin.argv = argv + optind - 1;
}
else
{
fname = argv[optind];
args->plugin.argc = argc - optind;
args->plugin.argv = argv + optind;
}
optind = 0;
args->files = bcf_sr_init();
if ( args->regions_list )
{
if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
error("Failed to read the regions: %s\n", args->regions_list);
}
if ( args->targets_list )
{
if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
error("Failed to read the targets: %s\n", args->targets_list);
args->files->collapse |= COLLAPSE_SOME;
}
if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
init_data(args);
while ( bcf_sr_next_line(args->files) )
{
bcf1_t *line = bcf_sr_get_line(args->files,0);
if ( args->filter )
{
int pass = filter_test(args->filter, line, NULL);
if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
if ( !pass ) continue;
}
line = args->plugin.process(line);
if ( line ) bcf_write1(args->out_fh, args->hdr_out, line);
}
destroy_data(args);
bcf_sr_destroy(args->files);
free(args);
return 0;
}
int run(int argc, char **argv)
{
char *trio_samples = NULL, *trio_file = NULL, *rules_fname = NULL, *rules_string = NULL;
memset(&args,0,sizeof(args_t));
args.mode = 0;
args.output_fname = "-";
static struct option loptions[] =
{
{"trio",1,0,'t'},
{"trio-file",1,0,'T'},
{"delete",0,0,'d'},
{"list",1,0,'l'},
{"count",0,0,'c'},
{"rules",1,0,'r'},
{"rules-file",1,0,'R'},
{"output",required_argument,NULL,'o'},
{"output-type",required_argument,NULL,'O'},
{0,0,0,0}
};
int c;
while ((c = getopt_long(argc, argv, "?ht:T:l:cdr:R:o:O:",loptions,NULL)) >= 0)
{
switch (c)
{
case 'o': args.output_fname = optarg; break;
case 'O':
switch (optarg[0]) {
case 'b': args.output_type = FT_BCF_GZ; break;
case 'u': args.output_type = FT_BCF; break;
case 'z': args.output_type = FT_VCF_GZ; break;
case 'v': args.output_type = FT_VCF; break;
default: error("The output type \"%s\" not recognised\n", optarg);
};
break;
case 'R': rules_fname = optarg; break;
case 'r': rules_string = optarg; break;
case 'd': args.mode |= MODE_DELETE; break;
case 'c': args.mode |= MODE_COUNT; break;
case 'l':
if ( !strcmp("+",optarg) ) args.mode |= MODE_LIST_GOOD;
else if ( !strcmp("x",optarg) ) args.mode |= MODE_LIST_BAD;
else error("The argument not recognised: --list %s\n", optarg);
break;
case 't': trio_samples = optarg; break;
case 'T': trio_file = optarg; break;
case 'h':
case '?':
default: error("%s",usage()); break;
}
}
if ( rules_fname )
args.rules = regidx_init(rules_fname, parse_rules, NULL, sizeof(rule_t), &args);
else
args.rules = init_rules(&args, rules_string);
if ( !args.rules ) return -1;
args.itr = regitr_init(args.rules);
args.itr_ori = regitr_init(args.rules);
char *fname = NULL;
if ( optind>=argc || argv[optind][0]=='-' )
{
if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin
else error("%s",usage());
}
else
fname = argv[optind];
if ( !trio_samples && !trio_file ) error("Expected the -t/T option\n");
if ( !args.mode ) error("Expected one of the -c, -d or -l options\n");
if ( args.mode&MODE_DELETE && !(args.mode&(MODE_LIST_GOOD|MODE_LIST_BAD)) ) args.mode |= MODE_LIST_GOOD|MODE_LIST_BAD;
args.sr = bcf_sr_init();
if ( !bcf_sr_add_reader(args.sr, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args.sr->errnum));
args.hdr = bcf_sr_get_header(args.sr, 0);
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);
int i, n = 0;
char **list;
if ( trio_samples )
{
args.ntrios = 1;
args.trios = (trio_t*) calloc(1,sizeof(trio_t));
list = hts_readlist(trio_samples, 0, &n);
if ( n!=3 ) error("Expected three sample names with -t\n");
args.trios[0].imother = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[0]);
args.trios[0].ifather = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[1]);
args.trios[0].ichild = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[2]);
for (i=0; i<n; i++) free(list[i]);
free(list);
}
if ( trio_file )
{
list = hts_readlist(trio_file, 1, &n);
args.ntrios = n;
args.trios = (trio_t*) calloc(n,sizeof(trio_t));
for (i=0; i<n; i++)
{
char *ss = list[i], *se;
se = strchr(ss, ',');
if ( !se ) error("Could not parse %s: %s\n",trio_file, ss);
*se = 0;
args.trios[i].imother = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, ss);
if ( args.trios[i].imother<0 ) error("No such sample: \"%s\"\n", ss);
ss = ++se;
se = strchr(ss, ',');
if ( !se ) error("Could not parse %s\n",trio_file);
*se = 0;
args.trios[i].ifather = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, ss);
if ( args.trios[i].ifather<0 ) error("No such sample: \"%s\"\n", ss);
ss = ++se;
if ( *ss=='\0' ) error("Could not parse %s\n",trio_file);
args.trios[i].ichild = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, ss);
if ( args.trios[i].ichild<0 ) error("No such sample: \"%s\"\n", ss);
free(list[i]);
}
free(list);
}
while ( bcf_sr_next_line(args.sr) )
{
bcf1_t *line = bcf_sr_get_line(args.sr,0);
line = process(line);
if ( line )
{
if ( line->errcode ) error("TODO: Unchecked error (%d), exiting\n",line->errcode);
bcf_write1(args.out_fh, args.hdr, line);
}
}
fprintf(stderr,"# [1]nOK\t[2]nBad\t[3]nSkipped\t[4]Trio\n");
for (i=0; i<args.ntrios; i++)
{
trio_t *trio = &args.trios[i];
fprintf(stderr,"%d\t%d\t%d\t%s,%s,%s\n",
trio->nok,trio->nbad,args.nrec-(trio->nok+trio->nbad),
bcf_hdr_int2id(args.hdr, BCF_DT_SAMPLE, trio->imother),
bcf_hdr_int2id(args.hdr, BCF_DT_SAMPLE, trio->ifather),
bcf_hdr_int2id(args.hdr, BCF_DT_SAMPLE, trio->ichild)
);
}
free(args.gt_arr);
free(args.trios);
regitr_destroy(args.itr);
regitr_destroy(args.itr_ori);
regidx_destroy(args.rules);
bcf_sr_destroy(args.sr);
if ( hts_close(args.out_fh)!=0 ) error("Error: close failed\n");
return 0;
}
int main_vcfview(int argc, char *argv[])
{
int c;
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->argc = argc; args->argv = argv;
args->files = bcf_sr_init();
args->clevel = -1;
args->print_header = 1;
args->update_info = 1;
args->output_type = FT_VCF;
int targets_is_file = 0, regions_is_file = 0;
static struct option loptions[] =
{
{"genotype",1,0,'g'},
{"compression-level",1,0,'l'},
{"header-only",0,0,'h'},
{"no-header",0,0,'H'},
{"exclude",1,0,'e'},
{"include",1,0,'i'},
{"trim-alt-alleles",0,0,'a'},
{"no-update",0,0,'I'},
{"drop-genotypes",0,0,'G'},
{"private",0,0,'x'},
{"exclude-private",0,0,'X'},
{"uncalled",0,0,'u'},
{"exclude-uncalled",0,0,'U'},
{"apply-filters",1,0,'f'},
{"known",0,0,'k'},
{"novel",0,0,'n'},
{"min-alleles",1,0,'m'},
{"max-alleles",1,0,'M'},
{"samples",1,0,'s'},
{"samples-file",1,0,'S'},
{"force-samples",0,0,1},
{"output-type",1,0,'O'},
{"output-file",1,0,'o'},
{"types",1,0,'v'},
{"exclude-types",1,0,'V'},
{"targets",1,0,'t'},
{"targets-file",1,0,'T'},
{"regions",1,0,'r'},
{"regions-file",1,0,'R'},
{"min-ac",1,0,'c'},
{"max-ac",1,0,'C'},
{"min-af",1,0,'q'},
{"max-af",1,0,'Q'},
{"phased",0,0,'p'},
{"exclude-phased",0,0,'P'},
{0,0,0,0}
};
char *tmp;
while ((c = getopt_long(argc, argv, "l:t:T:r:R:o:O:s:S:Gf:knv:V:m:M:auUhHc:C:Ii:e:xXpPq:Q:g:",loptions,NULL)) >= 0)
{
char allele_type[8] = "nref";
switch (c)
{
case 'O':
switch (optarg[0]) {
case 'b': args->output_type = FT_BCF_GZ; break;
case 'u': args->output_type = FT_BCF; break;
case 'z': args->output_type = FT_VCF_GZ; break;
case 'v': args->output_type = FT_VCF; break;
default: error("The output type \"%s\" not recognised\n", optarg);
};
break;
case 'l':
args->clevel = strtol(optarg,&tmp,10);
if ( *tmp ) error("Could not parse argument: --compression-level %s\n", optarg);
args->output_type |= FT_GZ;
break;
case 'o': args->fn_out = optarg; break;
case 'H': args->print_header = 0; break;
case 'h': args->header_only = 1; break;
case 't': args->targets_list = optarg; break;
case 'T': args->targets_list = optarg; targets_is_file = 1; break;
case 'r': args->regions_list = optarg; break;
case 'R': args->regions_list = optarg; regions_is_file = 1; break;
case 's': args->sample_names = optarg; break;
case 'S': args->sample_names = optarg; args->sample_is_file = 1; break;
case 1 : args->force_samples = 1; break;
case 'a': args->trim_alts = 1; args->calc_ac = 1; break;
case 'I': args->update_info = 0; break;
case 'G': args->sites_only = 1; break;
case 'f': args->files->apply_filters = optarg; break;
case 'k': args->known = 1; break;
case 'n': args->novel = 1; break;
case 'm':
args->min_alleles = strtol(optarg,&tmp,10);
if ( *tmp ) error("Could not parse argument: --min-alleles %s\n", optarg);
break;
case 'M':
args->max_alleles = strtol(optarg,&tmp,10);
if ( *tmp ) error("Could not parse argument: --max-alleles %s\n", optarg);
break;
case 'v': args->include_types = optarg; break;
case 'V': args->exclude_types = optarg; break;
case 'e': args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
case 'i': args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
case 'c':
{
args->min_ac_type = ALLELE_NONREF;
if ( sscanf(optarg,"%d:%s",&args->min_ac, allele_type)!=2 && sscanf(optarg,"%d",&args->min_ac)!=1 )
error("Error: Could not parse --min-ac %s\n", optarg);
set_allele_type(&args->min_ac_type, allele_type);
args->calc_ac = 1;
break;
}
case 'C':
{
args->max_ac_type = ALLELE_NONREF;
if ( sscanf(optarg,"%d:%s",&args->max_ac, allele_type)!=2 && sscanf(optarg,"%d",&args->max_ac)!=1 )
error("Error: Could not parse --max-ac %s\n", optarg);
set_allele_type(&args->max_ac_type, allele_type);
args->calc_ac = 1;
break;
}
case 'q':
{
args->min_af_type = ALLELE_NONREF;
if ( sscanf(optarg,"%f:%s",&args->min_af, allele_type)!=2 && sscanf(optarg,"%f",&args->min_af)!=1 )
error("Error: Could not parse --min_af %s\n", optarg);
set_allele_type(&args->min_af_type, allele_type);
args->calc_ac = 1;
break;
}
case 'Q':
{
args->max_af_type = ALLELE_NONREF;
if ( sscanf(optarg,"%f:%s",&args->max_af, allele_type)!=2 && sscanf(optarg,"%f",&args->max_af)!=1 )
error("Error: Could not parse --min_af %s\n", optarg);
set_allele_type(&args->max_af_type, allele_type);
args->calc_ac = 1;
break;
}
case 'x': args->private_vars |= FLT_INCLUDE; args->calc_ac = 1; break;
case 'X': args->private_vars |= FLT_EXCLUDE; args->calc_ac = 1; break;
case 'u': args->uncalled |= FLT_INCLUDE; args->calc_ac = 1; break;
case 'U': args->uncalled |= FLT_EXCLUDE; args->calc_ac = 1; break;
case 'p': args->phased |= FLT_INCLUDE; break; // phased
case 'P': args->phased |= FLT_EXCLUDE; break; // exclude-phased
case 'g':
{
if ( !strcasecmp(optarg,"hom") ) args->gt_type = GT_NEED_HOM;
else if ( !strcasecmp(optarg,"het") ) args->gt_type = GT_NEED_HET;
else if ( !strcasecmp(optarg,"miss") ) args->gt_type = GT_NEED_MISSING;
else if ( !strcasecmp(optarg,"^hom") ) args->gt_type = GT_NO_HOM;
else if ( !strcasecmp(optarg,"^het") ) args->gt_type = GT_NO_HET;
else if ( !strcasecmp(optarg,"^miss") ) args->gt_type = GT_NO_MISSING;
else error("The argument to -g not recognised. Expected one of hom/het/miss/^hom/^het/^miss, got \"%s\".\n", optarg);
break;
}
case '?': usage(args);
default: error("Unknown argument: %s\n", optarg);
}
}
if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n");
if ( args->private_vars > FLT_EXCLUDE ) error("Only one of -x or -X can be given.\n");
if ( args->uncalled > FLT_EXCLUDE ) error("Only one of -u or -U can be given.\n");
if ( args->phased > FLT_EXCLUDE ) error("Only one of -p or -P can be given.\n");
if ( args->sample_names && args->update_info) args->calc_ac = 1;
char *fname = NULL;
if ( optind>=argc )
{
if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin
else usage(args);
}
else fname = argv[optind];
// read in the regions from the command line
if ( args->regions_list )
{
if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
error("Failed to read the regions: %s\n", args->regions_list);
}
else if ( optind+1 < argc )
{
int i;
kstring_t tmp = {0,0,0};
kputs(argv[optind+1],&tmp);
for (i=optind+2; i<argc; i++) { kputc(',',&tmp); kputs(argv[i],&tmp); }
if ( bcf_sr_set_regions(args->files, tmp.s, 0)<0 )
error("Failed to read the regions: %s\n", tmp.s);
free(tmp.s);
}
if ( args->targets_list )
{
if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
error("Failed to read the targets: %s\n", args->targets_list);
}
if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
init_data(args);
bcf_hdr_t *out_hdr = args->hnull ? args->hnull : (args->hsub ? args->hsub : args->hdr);
if (args->print_header)
bcf_hdr_write(args->out, out_hdr);
else if ( args->output_type & FT_BCF )
error("BCF output requires header, cannot proceed with -H\n");
if (!args->header_only)
{
while ( bcf_sr_next_line(args->files) )
{
bcf1_t *line = args->files->readers[0].buffer[0];
if ( line->errcode && out_hdr!=args->hdr ) error("Undefined tags in the header, cannot proceed in the sample subset mode.\n");
if ( subset_vcf(args, line) )
bcf_write1(args->out, out_hdr, line);
}
}
hts_close(args->out);
destroy_data(args);
bcf_sr_destroy(args->files);
free(args);
return 0;
}
int main_vcfroh(int argc, char *argv[])
{
int c;
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->argc = argc; args->argv = argv;
args->files = bcf_sr_init();
args->t2AZ = 6.7e-8;
args->t2HW = 5e-9;
args->rec_rate = 0;
int regions_is_file = 0, targets_is_file = 0;
static struct option loptions[] =
{
{"AF-tag",1,0,0},
{"AF-file",1,0,1},
{"AF-dflt",1,0,2},
{"estimate-AF",1,0,'e'},
{"GTs-only",1,0,'G'},
{"sample",1,0,'s'},
{"hw-to-az",1,0,'a'},
{"az-to-hw",1,0,'H'},
{"viterbi-training",0,0,'V'},
{"targets",1,0,'t'},
{"targets-file",1,0,'T'},
{"regions",1,0,'r'},
{"regions-file",1,0,'R'},
{"genetic-map",1,0,'m'},
{"rec-rate",1,0,'M'},
{"skip-indels",0,0,'I'},
{0,0,0,0}
};
int naf_opts = 0;
char *tmp;
while ((c = getopt_long(argc, argv, "h?r:R:t:T:H:a:s:m:M:G:Ia:e:V",loptions,NULL)) >= 0) {
switch (c) {
case 0: args->af_tag = optarg; naf_opts++; break;
case 1: args->af_fname = optarg; naf_opts++; break;
case 2:
args->dflt_AF = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse: --AF-dflt %s\n", optarg);
break;
case 'e': args->estimate_AF = optarg; naf_opts++; break;
case 'I': args->snps_only = 1; break;
case 'G':
args->fake_PLs = 1;
args->unseen_PL = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse: -G %s\n", optarg);
args->unseen_PL = pow(10,-args->unseen_PL/10.);
break;
case 'm': args->genmap_fname = optarg; break;
case 'M':
args->rec_rate = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse: -M %s\n", optarg);
break;
case 's': args->sample = strdup(optarg); break;
case 'a':
args->t2AZ = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse: -a %s\n", optarg);
break;
case 'H':
args->t2HW = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse: -H %s\n", optarg);
break;
case 't': args->targets_list = optarg; break;
case 'T': args->targets_list = optarg; targets_is_file = 1; break;
case 'r': args->regions_list = optarg; break;
case 'R': args->regions_list = optarg; regions_is_file = 1; break;
case 'V': args->vi_training = 1; break;
case 'h':
case '?': usage(args); break;
default: error("Unknown argument: %s\n", optarg);
}
}
if ( argc<optind+1 ) usage(args);
if ( args->t2AZ<0 || args->t2AZ>1 ) error("Error: The parameter --hw-to-az is not in [0,1]\n", args->t2AZ);
if ( args->t2HW<0 || args->t2HW>1 ) error("Error: The parameter --az-to-hw is not in [0,1]\n", args->t2HW);
if ( naf_opts>1 ) error("Error: The options --AF-tag, --AF-file and -e are mutually exclusive\n");
if ( args->af_fname && args->targets_list ) error("Error: The options --AF-file and -t are mutually exclusive\n");
if ( args->regions_list )
{
if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
error("Failed to read the regions: %s\n", args->regions_list);
}
if ( args->targets_list )
{
if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
error("Failed to read the targets: %s\n", args->targets_list);
}
if ( args->af_fname )
{
if ( bcf_sr_set_targets(args->files, args->af_fname, 1, 3)<0 )
error("Failed to read the targets: %s\n", args->af_fname);
}
if ( !bcf_sr_add_reader(args->files, argv[optind]) ) error("Failed to open %s: %s\n", argv[optind],bcf_sr_strerror(args->files->errnum));
init_data(args);
while ( bcf_sr_next_line(args->files) )
{
vcfroh(args, args->files->readers[0].buffer[0]);
}
vcfroh(args, NULL);
fprintf(pysamerr,"Number of lines: total/processed: %d/%d\n", args->ntot,args->nused);
destroy_data(args);
free(args);
return 0;
}
int main_vcfquery(int argc, char *argv[])
{
int c, collapse = 0;
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->argc = argc; args->argv = argv;
int regions_is_file = 0, targets_is_file = 0;
static struct option loptions[] =
{
{"help",0,0,'h'},
{"list-samples",0,0,'l'},
{"include",1,0,'i'},
{"exclude",1,0,'e'},
{"format",1,0,'f'},
{"output-file",1,0,'o'},
{"regions",1,0,'r'},
{"regions-file",1,0,'R'},
{"targets",1,0,'t'},
{"targets-file",1,0,'T'},
{"annots",1,0,'a'},
{"samples",1,0,'s'},
{"samples-file",1,0,'S'},
{"print-header",0,0,'H'},
{"collapse",1,0,'c'},
{"vcf-list",1,0,'v'},
{"allow-undef-tags",0,0,'u'},
{0,0,0,0}
};
while ((c = getopt_long(argc, argv, "hlr:R:f:a:s:S:Ht:T:c:v:i:e:o:u",loptions,NULL)) >= 0) {
switch (c) {
case 'o': args->fn_out = optarg; break;
case 'f': args->format_str = strdup(optarg); break;
case 'H': args->print_header = 1; break;
case 'v': args->vcf_list = optarg; break;
case 'c':
if ( !strcmp(optarg,"snps") ) collapse |= COLLAPSE_SNPS;
else if ( !strcmp(optarg,"indels") ) collapse |= COLLAPSE_INDELS;
else if ( !strcmp(optarg,"both") ) collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS;
else if ( !strcmp(optarg,"any") ) collapse |= COLLAPSE_ANY;
else if ( !strcmp(optarg,"all") ) collapse |= COLLAPSE_ANY;
else if ( !strcmp(optarg,"some") ) collapse |= COLLAPSE_SOME;
else error("The --collapse string \"%s\" not recognised.\n", optarg);
break;
case 'a':
{
kstring_t str = {0,0,0};
kputs("%CHROM\t%POS\t%MASK\t%REF\t%ALT\t%", &str);
char *p = optarg;
while ( *p )
{
if ( *p==',' )
kputs("\t%", &str);
else
kputc(*p, &str);
p++;
}
kputc('\n', &str);
args->format_str = str.s;
break;
}
case 'e': args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
case 'i': args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
case 'r': args->regions_list = optarg; break;
case 'R': args->regions_list = optarg; regions_is_file = 1; break;
case 't': args->targets_list = optarg; break;
case 'T': args->targets_list = optarg; targets_is_file = 1; break;
case 'l': args->list_columns = 1; break;
case 'u': args->allow_undef_tags = 1; break;
case 's': args->sample_list = optarg; break;
case 'S': args->sample_list = optarg; args->sample_is_file = 1; break;
case 'h':
case '?': usage();
default: error("Unknown argument: %s\n", optarg);
}
}
char *fname = NULL;
if ( optind>=argc )
{
if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";
}
else fname = argv[optind];
if ( args->list_columns )
{
if ( !fname ) error("Missing the VCF file name\n");
args->files = bcf_sr_init();
if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
list_columns(args);
bcf_sr_destroy(args->files);
free(args);
return 0;
}
if ( !args->format_str ) usage();
args->out = args->fn_out ? fopen(args->fn_out, "w") : stdout;
if ( !args->out ) error("%s: %s\n", args->fn_out,strerror(errno));
if ( !args->vcf_list )
{
if ( !fname ) usage();
args->files = bcf_sr_init();
args->files->collapse = collapse;
if ( optind+1 < argc ) args->files->require_index = 1;
if ( args->regions_list && bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
error("Failed to read the regions: %s\n", args->regions_list);
if ( args->targets_list )
{
if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
error("Failed to read the targets: %s\n", args->targets_list);
}
while ( fname )
{
if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
fname = ++optind < argc ? argv[optind] : NULL;
}
init_data(args);
query_vcf(args);
free(args->format_str);
destroy_data(args);
bcf_sr_destroy(args->files);
fclose(args->out);
free(args);
return 0;
}
// multiple VCFs
int i, k, nfiles, prev_nsamples = 0;
char **fnames, **prev_samples = NULL;
fnames = hts_readlist(args->vcf_list, 1, &nfiles);
if ( !nfiles ) error("No files in %s?\n", args->vcf_list);
for (i=0; i<nfiles; i++)
{
args->files = bcf_sr_init();
args->files->collapse = collapse;
if ( args->regions_list && bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
error("Failed to read the regions: %s\n", args->regions_list);
if ( optind < argc ) args->files->require_index = 1;
if ( args->targets_list )
{
if ( bcf_sr_set_targets(args->files, args->targets_list,targets_is_file, 0)<0 )
error("Failed to read the targets: %s\n", args->targets_list);
}
if ( !bcf_sr_add_reader(args->files, fnames[i]) ) error("Failed to open %s: %s\n", fnames[i],bcf_sr_strerror(args->files->errnum));
for (k=optind; k<argc; k++)
if ( !bcf_sr_add_reader(args->files, argv[k]) ) error("Failed to open %s: %s\n", argv[k],bcf_sr_strerror(args->files->errnum));
init_data(args);
if ( i==0 )
prev_samples = copy_header(args->header, args->files->readers[0].header->samples, bcf_hdr_nsamples(args->files->readers[0].header));
else
{
args->print_header = 0;
if ( compare_header(args->header, args->files->readers[0].header->samples, bcf_hdr_nsamples(args->files->readers[0].header), prev_samples, prev_nsamples) )
error("Different samples in %s and %s\n", fnames[i-1],fnames[i]);
}
query_vcf(args);
destroy_data(args);
bcf_sr_destroy(args->files);
}
fclose(args->out);
destroy_list(fnames, nfiles);
destroy_list(prev_samples, prev_nsamples);
free(args->format_str);
free(args);
return 0;
}
int run(int argc, char **argv)
{
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->nsites = 10;
args->min_hets = 0.3;
args->background = "X:60001-2699520";
static struct option loptions[] =
{
{"verbose",1,0,'v'},
{"ploidy",1,0,'p'},
{"nsites",1,0,'n'},
{"guess",1,0,'g'},
{"min-hets",1,0,'m'},
{"background",1,0,'b'},
{0,0,0,0}
};
char c, *tmp, *ploidy_fname = NULL;
while ((c = getopt_long(argc, argv, "p:n:g:m:vb:",loptions,NULL)) >= 0)
{
switch (c) {
case 'b':
if ( !strcmp("-",optarg) ) args->background = NULL;
else args->background = optarg;
break;
case 'v': args->verbose = 1; break;
case 'g':
if ( !strcasecmp(optarg,"GT") ) args->guess = GUESS_GT;
else if ( !strcasecmp(optarg,"PL") ) args->guess = GUESS_PL;
else if ( !strcasecmp(optarg,"GL") ) args->guess = GUESS_GL;
else error("The argument not recognised, expected --guess GT, --guess PL or --guess GL: %s\n", optarg);
break;
case 'm':
args->min_hets = strtod(optarg,&tmp);
if ( *tmp ) error("Unexpected argument to --min-hets: %s\n", optarg);
break;
case 'p': ploidy_fname = optarg; break;
case 'n':
args->nsites = strtol(optarg,&tmp,10);
if (*tmp) error("Unexpected argument to --nsites: %s\n", optarg); break;
case 'h':
case '?':
default: error("%s", usage()); break;
}
}
args->sr = bcf_sr_init();
args->sr->require_index = 1;
if ( !argv[0] ) error("%s", usage());
if ( !bcf_sr_add_reader(args->sr,argv[0]) ) error("Error: %s\n", bcf_sr_strerror(args->sr->errnum));
args->hdr = args->sr->readers[0].header;
args->nsample = bcf_hdr_nsamples(args->hdr);
args->dflt_ploidy = 2;
if ( ploidy_fname )
{
args->ploidy = ploidy_init(ploidy_fname, args->dflt_ploidy);
if ( !args->ploidy ) error("Could not read %s\n", ploidy_fname);
}
else
{
args->ploidy = ploidy_init_string(
"X 1 60000 M 1\n"
"X 2699521 154931043 M 1\n"
"Y 1 59373566 M 1\n"
"Y 1 59373566 F 0\n", args->dflt_ploidy);
}
args->nsex = ploidy_nsex(args->ploidy);
args->sex2ploidy = (int*) malloc(sizeof(int)*args->nsex);
args->max_ploidy = ploidy_max(args->ploidy);
if ( args->guess && args->max_ploidy > 2 ) error("Sorry, ploidy %d not supported with -g\n", args->max_ploidy);
args->ncounts = args->nsample * ((args->max_ploidy>2 ? args->max_ploidy : 2)+1);
args->counts = (int*) malloc(sizeof(int)*args->ncounts);
args->bg_counts = (count_t*) calloc(args->nsample,sizeof(count_t));
args->sex2prob = (float*) calloc(args->nsample*args->nsex,sizeof(float));
int i, nseq;
for (i=0; i<args->nsample*args->nsex; i++) args->sex2prob[i] = 1;
if ( args->verbose && args->guess )
printf("# [1]REG\t[2]Region\t[3]Sample\t[4]Het fraction\t[5]nHet\t[6]nHom\t[7]nMissing\n");
// First get the counts from expected haploid regions
regidx_t *idx = ploidy_regions(args->ploidy);
char **seqs = regidx_seq_names(idx, &nseq);
for (i=0; i<nseq; i++)
{
regitr_t itr;
regidx_overlap(idx, seqs[i], 0, UINT32_MAX, &itr);
while ( itr.i < itr.n )
{
if ( args->guess )
itr.i += process_region_guess(args, seqs[i], &itr);
else
itr.i += process_region_precise(args, seqs[i], &itr);
}
}
// Get the counts from a PAR (the background diploid region) and see if the fraction
// of hets is different
if ( args->guess ) sex2prob_guess(args);
for (i=0; i<args->nsample; i++)
{
int j, jmax = 0;
float max = 0, sum = 0;
for (j=0; j<args->nsex; j++)
{
sum += args->sex2prob[i*args->nsex+j];
if ( max < args->sex2prob[i*args->nsex+j] )
{
jmax = j;
max = args->sex2prob[i*args->nsex+j];
}
}
if ( args->verbose )
printf("%s\t%s\t%f\n", args->hdr->samples[i],ploidy_id2sex(args->ploidy,jmax),args->sex2prob[i*args->nsex+jmax]/sum);
else
printf("%s\t%s\n", args->hdr->samples[i],ploidy_id2sex(args->ploidy,jmax));
}
bcf_sr_destroy(args->sr);
ploidy_destroy(args->ploidy);
destroy_regs(args);
free(args->sex2ploidy);
free(args->counts);
free(args->bg_counts);
free(args->gts);
free(args->pls);
free(args->sex2prob);
free(args);
return 0;
}
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);
}