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);
}
