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; 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'}, {"targets",1,0,'t'}, {0,0,0,0} }; while ((c = getopt_long(argc, argv, "hg:p:s:S:Hr:at:G:",loptions,NULL)) >= 0) { switch (c) { case 'G': args->no_PLs = atoi(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 't': targets = optarg; break; case 'h': case '?': usage(); default: error("Unknown argument: %s\n", optarg); } } if ( argc==optind || argc>optind+1 ) usage(); // none or 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)<0 ) error("Failed to read the regions: %s\n", regions); if ( targets && bcf_sr_set_targets(args->files, targets,0)<0 ) error("Failed to read the targets: %s\n", targets); if ( !bcf_sr_add_reader(args->files, argv[optind]) ) error("Failed to open or the file not indexed: %s\n", argv[optind]); if ( args->gt_fname && !bcf_sr_add_reader(args->files, args->gt_fname) ) error("Failed to open or the file not indexed: %s\n", args->gt_fname); 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->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); }
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) { 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; } }
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; }
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->files = bcf_sr_init(); args->output_fname = "-"; args->output_type = FT_VCF; args->nplugin_paths = -1; int regions_is_file = 0, targets_is_file = 0, plist_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[] = { {"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:li:e:v",loptions,NULL)) >= 0) { switch (c) { 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': load_plugin(args, plugin_name, 1, &args->plugin); fprintf(stderr,"%s",args->plugin.usage()); return 0; break; default: error("Unknown argument: %s\n", optarg); } } if ( plist_only ) return list_plugins(args); 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->plugin.argv[0] = plugin_name; load_plugin(args, plugin_name, 1, &args->plugin); 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 or the file not indexed: %s\n", fname); 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 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; }
void set_target(const std::string ®ion) { if (bcf_sr_set_targets(m_sr, region.c_str(), false, 0) != 0) throw std::runtime_error("Could not set target: [" + region + "]"); assert(m_sr->require_index == 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); }