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;
}
int main_vcfcall(int argc, char *argv[])
{
char *ploidy_fname = NULL, *ploidy = NULL;
args_t args;
memset(&args, 0, sizeof(args_t));
args.argc = argc; args.argv = argv;
args.aux.prior_type = -1;
args.aux.indel_frac = -1;
args.aux.theta = 1.1e-3;
args.aux.pref = 0.5;
args.aux.min_perm_p = 0.01;
args.aux.min_lrt = 1;
args.flag = CF_ACGT_ONLY;
args.output_fname = "-";
args.output_type = FT_VCF;
args.aux.trio_Pm_SNPs = 1 - 1e-8;
args.aux.trio_Pm_ins = args.aux.trio_Pm_del = 1 - 1e-9;
int c;
static struct option loptions[] =
{
{"help",0,0,'h'},
{"gvcf",1,0,'g'},
{"format-fields",1,0,'f'},
{"output",1,0,'o'},
{"output-type",1,0,'O'},
{"regions",1,0,'r'},
{"regions-file",1,0,'R'},
{"samples",1,0,'s'},
{"samples-file",1,0,'S'},
{"targets",1,0,'t'},
{"targets-file",1,0,'T'},
{"keep-alts",0,0,'A'},
{"insert-missed",0,0,'i'},
{"skip-Ns",0,0,'N'}, // now the new default
{"keep-masked-refs",0,0,'M'},
{"skip-variants",1,0,'V'},
{"variants-only",0,0,'v'},
{"consensus-caller",0,0,'c'},
{"constrain",1,0,'C'},
{"multiallelic-caller",0,0,'m'},
{"pval-threshold",1,0,'p'},
{"prior",1,0,'P'},
{"chromosome-X",0,0,'X'},
{"chromosome-Y",0,0,'Y'},
{"novel-rate",1,0,'n'},
{"ploidy",1,0,1},
{"ploidy-file",1,0,2},
{0,0,0,0}
};
char *tmp = NULL;
while ((c = getopt_long(argc, argv, "h?o:O:r:R:s:S:t:T:ANMV:vcmp:C:XYn:P:f:ig:", loptions, NULL)) >= 0)
{
switch (c)
{
case 'g':
args.flag |= CF_GVCF;
args.gvcf.min_dp = strtol(optarg,&tmp,10);
if ( *tmp ) error("Could not parse, expected integer argument: -g %s\n", optarg);
break;
case 2 : ploidy_fname = optarg; break;
case 1 : ploidy = optarg; break;
case 'X': ploidy = "X"; fprintf(stderr,"Warning: -X will be deprecated, please use --ploidy instead.\n"); break;
case 'Y': ploidy = "Y"; fprintf(stderr,"Warning: -Y will be deprecated, please use --ploidy instead.\n"); break;
case 'f': args.aux.output_tags |= parse_format_flag(optarg); break;
case 'M': args.flag &= ~CF_ACGT_ONLY; break; // keep sites where REF is N
case 'N': args.flag |= CF_ACGT_ONLY; break; // omit sites where first base in REF is N (the new default)
case 'A': args.aux.flag |= CALL_KEEPALT; break;
case 'c': args.flag |= CF_CCALL; break; // the original EM based calling method
case 'i': args.flag |= CF_INS_MISSED; break;
case 'v': args.aux.flag |= CALL_VARONLY; 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 'C':
if ( !strcasecmp(optarg,"alleles") ) args.aux.flag |= CALL_CONSTR_ALLELES;
else if ( !strcasecmp(optarg,"trio") ) args.aux.flag |= CALL_CONSTR_TRIO;
else error("Unknown argument to -C: \"%s\"\n", optarg);
break;
case 'V':
if ( !strcasecmp(optarg,"snps") ) args.flag |= CF_INDEL_ONLY;
else if ( !strcasecmp(optarg,"indels") ) args.flag |= CF_NO_INDEL;
else error("Unknown skip category \"%s\" (-S argument must be \"snps\" or \"indels\")\n", optarg);
break;
case 'm': args.flag |= CF_MCALL; break; // multiallelic calling method
case 'p':
args.aux.pref = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse: --pval-threshold %s\n", optarg);
break;
case 'P': args.aux.theta = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse, expected float argument: -P %s\n", optarg);
break;
case 'n': parse_novel_rate(&args,optarg); break;
case 'r': args.regions = optarg; break;
case 'R': args.regions = optarg; args.regions_is_file = 1; break;
case 't': args.targets = optarg; break;
case 'T': args.targets = optarg; args.targets_is_file = 1; break;
case 's': args.samples_fname = optarg; break;
case 'S': args.samples_fname = optarg; args.samples_is_file = 1; break;
default: usage(&args);
}
}
// Sanity check options and initialize
if ( ploidy_fname ) args.ploidy = ploidy_init(ploidy_fname, 2);
else if ( ploidy ) args.ploidy = init_ploidy(ploidy);
if ( optind>=argc )
{
if ( !isatty(fileno((FILE *)stdin)) ) args.bcf_fname = "-"; // reading from stdin
else usage(&args);
}
else args.bcf_fname = argv[optind++];
if ( !ploidy_fname && !ploidy )
{
fprintf(stderr,"Note: Neither --ploidy nor --ploidy-file given, assuming all sites are diploid\n");
args.ploidy = ploidy_init_string("",2);
}
if ( !args.ploidy ) error("Could not initialize ploidy\n");
if ( args.flag & CF_GVCF )
{
// Force some flags to avoid unnecessary branching
args.aux.flag &= ~CALL_KEEPALT;
args.aux.flag |= CALL_VARONLY;
}
if ( (args.flag & CF_CCALL ? 1 : 0) + (args.flag & CF_MCALL ? 1 : 0) + (args.flag & CF_QCALL ? 1 : 0) > 1 ) error("Only one of -c or -m options can be given\n");
if ( !(args.flag & CF_CCALL) && !(args.flag & CF_MCALL) && !(args.flag & CF_QCALL) ) error("Expected -c or -m option\n");
if ( args.aux.n_perm && args.aux.ngrp1_samples<=0 ) error("Expected -1 with -U\n"); // not sure about this, please fix
if ( args.aux.flag & CALL_CONSTR_ALLELES )
{
if ( !args.targets ) error("Expected -t or -T with \"-C alleles\"\n");
if ( !(args.flag & CF_MCALL) ) error("The \"-C alleles\" mode requires -m\n");
}
if ( args.flag & CF_INS_MISSED && !(args.aux.flag&CALL_CONSTR_ALLELES) ) error("The -i option requires -C alleles\n");
init_data(&args);
while ( bcf_sr_next_line(args.aux.srs) )
{
bcf1_t *bcf_rec = args.aux.srs->readers[0].buffer[0];
if ( args.samples_map ) bcf_subset(args.aux.hdr, bcf_rec, args.nsamples, args.samples_map);
bcf_unpack(bcf_rec, BCF_UN_STR);
// Skip unwanted sites
if ( args.aux.flag & CALL_VARONLY )
{
int is_ref = 0;
if ( bcf_rec->n_allele==1 ) is_ref = 1; // not a variant
else if ( bcf_rec->n_allele==2 )
{
// second allele is mpileup's X, not a variant
if ( bcf_rec->d.allele[1][0]=='X' ) is_ref = 1;
else if ( bcf_rec->d.allele[1][0]=='<' && bcf_rec->d.allele[1][1]=='X' && bcf_rec->d.allele[1][2]=='>' ) is_ref = 1;
else if ( bcf_rec->d.allele[1][0]=='<' && bcf_rec->d.allele[1][1]=='*' && bcf_rec->d.allele[1][2]=='>' ) is_ref = 1;
}
if ( is_ref )
{
// gVCF output
if ( args.flag & CF_GVCF ) gvcf_write(args.out_fh, &args.gvcf, args.aux.hdr, bcf_rec, 1);
continue;
}
}
if ( (args.flag & CF_INDEL_ONLY) && bcf_is_snp(bcf_rec) ) continue; // not an indel
if ( (args.flag & CF_NO_INDEL) && !bcf_is_snp(bcf_rec) ) continue; // not a SNP
if ( (args.flag & CF_ACGT_ONLY) && (bcf_rec->d.allele[0][0]=='N' || bcf_rec->d.allele[0][0]=='n') ) continue; // REF[0] is 'N'
bcf_unpack(bcf_rec, BCF_UN_ALL);
if ( args.nsex ) set_ploidy(&args, bcf_rec);
// Various output modes: QCall output (todo)
if ( args.flag & CF_QCALL )
{
qcall(&args.aux, bcf_rec);
continue;
}
// Calling modes which output VCFs
int ret;
if ( args.flag & CF_MCALL )
ret = mcall(&args.aux, bcf_rec);
else
ret = ccall(&args.aux, bcf_rec);
if ( ret==-1 ) error("Something is wrong\n");
// gVCF output
if ( args.flag & CF_GVCF )
{
gvcf_write(args.out_fh, &args.gvcf, args.aux.hdr, bcf_rec, ret?0:1);
continue;
}
// Normal output
if ( (args.aux.flag & CALL_VARONLY) && ret==0 ) continue; // not a variant
bcf_write1(args.out_fh, args.aux.hdr, bcf_rec);
}
if ( args.flag & CF_GVCF ) gvcf_write(args.out_fh, &args.gvcf, args.aux.hdr, NULL, 0);
if ( args.flag & CF_INS_MISSED ) bcf_sr_regions_flush(args.aux.srs->targets);
destroy_data(&args);
return 0;
}