// return true if current position in record is valid and usable
bool
site_crawler::
process_record_line(char* line)
{
static const unsigned MAX_WORD(50);
// do a low-level tab parse:
{
char* p(line);
_word[0]=p;
_n_word=1;
while (true) {
if ((*p == '\n') || (*p == '\0')) break;
if (*p == sep) {
*p = '\0';
_word[_n_word++] = p+1;
if (_n_word == MAX_WORD) break;
}
++p;
}
// allow for optional extra columns in each file format:
if (_n_word<_opt.sti().col_count()) {
log_os << "ERROR: Consensus record has " << _n_word << " column(s) but expecting at least " << _opt.sti().col_count() << "\n";
dump_state(log_os);
exit(EXIT_FAILURE);
}
}
const vcf_pos last_vpos(vpos());
_chrom=_opt.sti().chrom(_word);
_vpos.pos=_opt.sti().pos(_word);
_is_site_allele_current=false;
_is_indel_allele_current=false;
_vpos.is_indel=(_opt.sti().get_is_indel(_word));
if (pos()<1) {
log_os << "ERROR: gvcf record position less than 1. position: " << pos() << " ";
dump_state(log_os);
exit(EXIT_FAILURE);
}
if (_opt.is_region()) {
// deal with vcf records after the region of interest:
if (pos()>_opt.region_end) {
_is_sample_begin_state = false;
_is_sample_end_state = true;
return true;
}
} else {
if (pos()>static_cast<pos_t>(_ref_seg.end())) {
log_os << "ERROR: allele file position exceeds final position in reference sequence segment . position: "
<< pos() << " ref_contig_end: " << _ref_seg.end() << "\n";
dump_state(log_os);
exit(EXIT_FAILURE);
}
}
if (! _opt.sti().get_nonindel_ref_length(pos(),is_indel(),_word,_locus_size)) {
//log_os << "ERROR: failed to parse locus at pos: " << pos << "\n";
log_os << "WARNING: failed to parse locus at: " << vpos() << "\n";
dump_state(log_os);
//exit(EXIT_FAILURE);
_locus_size=0;
}
_locus_offset=0;
// deal with vcf records which fully proceed the region of interest:
if (_opt.is_region()) {
if ((pos()+_locus_size-1)<_opt.region_begin) return false;
}
//const bool last_is_call(is_call);
_is_call = _opt.sti().get_is_call(_word,pos(),_skip_call_begin_pos,_skip_call_end_pos);
_n_total = _opt.sti().total(_word);
if (is_indel()) {
if (! _is_return_indels)
{
_vpos.pos=last_vpos.pos;
_locus_size=0;
return false;
}
else
{
_locus_size=0;
}
}
if (is_any_call()) {
_is_call=update_allele();
}
// don't allow failed block read-through, so that we can get through indel-overlap errors
//if(! is_call) {
// if(_locus_size>1) _locus_size=1;
//}
if (! _is_sample_begin_state) {
if (! (last_vpos < vpos()) ) {
if (_opt.is_murdock_mode) {
_vpos=last_vpos;
_locus_size=0;
return false;
} else {
log_os << "ERROR: unexpected position order in variant file. current_pos: "
<< pos() << " last " << last_vpos << "\n";
dump_state(log_os);
exit(EXIT_FAILURE);
}
}
} else {
_is_sample_begin_state=false;
}
// deal with vcf records which partially overlap the region of interest:
if (_opt.is_region()) {
if (pos()<_opt.region_begin) return false;
}
return true;
}
//if you want to simulate a true hom, pass in var with both alleles the same
void simulator(int depth, int read_len, int kmer, double seq_err_per_base,
int number_repetitions, int colour_indiv,
int colour_allele1, int colour_allele2, int colour_ref_minus_site,
VariantBranchesAndFlanks* var,
int len_genome_minus_site, zygosity true_gt,
GraphAndModelInfo* model_info,
char* fasta, char* true_ml_gt_name,
int working_colour1, int working_colour2,
boolean using_1and2_nets,
dBGraph* db_graph)
//dBNode** genome_minus_site
//boolean are_the_two_alleles_identical
//char* filelist_net1, char* filelist_net2
//int working_colour_1net, int working_colour_2net
{
if (NUMBER_OF_COLOURS<4)
{
die("Cannot run the simulator with <4 colours. Recompile.\n");
}
int count_passes = 0;
int count_fails = 0;
const gsl_rng_type * T;
gsl_rng * r;
// GLS setup:
/* create a generator chosen by the
environment variable GSL_RNG_TYPE */
gsl_rng_env_setup();
T = gsl_rng_default;
r = gsl_rng_alloc (T);
//put the alleles and reference into their colours:
mark_allele_with_all_1s_or_more(var->one_allele, var->len_one_allele, colour_allele1);
mark_allele_with_all_1s_or_more(var->other_allele, var->len_other_allele, colour_allele2);
int i;
for (i=0; i<number_repetitions; i++)
{
zero_path_except_two_alleles_and_ref(var->one_allele, var->len_one_allele, colour_allele1, colour_allele2, colour_ref_minus_site);
zero_path_except_two_alleles_and_ref(var->other_allele, var->len_other_allele, colour_allele1, colour_allele2, colour_ref_minus_site);
//give the each allele depth which is taken from a Poisson with mean = (D/2) * (R-k+1)/R * (1-k*epsilon)
//printf("Depth %d, var->len one allele - k,er +1 = %d, and 1-kmer * seq_err = %f \n", depth, (var->len_one_allele)-kmer+1, 1-kmer*seq_err_per_base ) ;
double exp_depth_on_allele1 = 0;
if (true_gt==het)
//het. So 1/3 of seq errors on the other allele end up on this one
{
exp_depth_on_allele1 = ((double) depth/2) *
( (double)(read_len+(var->len_one_allele)-kmer+1)/read_len) * (1-kmer*seq_err_per_base);
// + ((double) depth/2) *
//( (double)(read_len+(var->len_other_allele)-kmer+1)/read_len) * (kmer*seq_err_per_base/3); //some errors from the other allele give covg here
}
else if (true_gt==hom_one)
{//hom
exp_depth_on_allele1 = ((double) depth) *
( (double)(read_len+(var->len_one_allele)-kmer+1)/read_len) * (1-kmer*seq_err_per_base);
}
else if (true_gt==hom_other)
{
exp_depth_on_allele1 = ((double) depth) *
( (double)(read_len+(var->len_other_allele)-kmer+1)/read_len) * kmer*seq_err_per_base/3;// 1/3 of the errors on the true allele are on this one
}
double exp_depth_on_allele2 = 0;
if (true_gt==het)
//het. So 1/3 of seq errors are not a problem. So loss of covg is (1-k*(2/3)*e)
{
exp_depth_on_allele2 = exp_depth_on_allele1;
}
else if (true_gt==hom_one)
{
exp_depth_on_allele2 = ( (double)(read_len+(var->len_one_allele)-kmer+1)/read_len) * kmer*seq_err_per_base/3;
}
else if (true_gt==hom_other)
{
exp_depth_on_allele2 = ((double) depth) *
( (double)(read_len+(var->len_other_allele)-kmer+1)/read_len) * (1-kmer*seq_err_per_base);
}
double exp_depth_on_ref_minus_site = (double) depth * ((double)(len_genome_minus_site-kmer+1)/read_len) * (1-kmer*seq_err_per_base);
//printf("exp ZAMMER %f %f %f\n", exp_depth_on_allele1, exp_depth_on_allele2, exp_depth_on_ref_minus_site);
unsigned int sampled_covg_allele1 = gsl_ran_poisson (r, exp_depth_on_allele1);
unsigned int sampled_covg_allele2 = gsl_ran_poisson (r, exp_depth_on_allele2);
unsigned int sampled_covg_rest_of_genome = gsl_ran_poisson (r, exp_depth_on_ref_minus_site);
printf("Sampled covgs on alleles 1,2 and genome are %d %d %d\n", sampled_covg_allele1, sampled_covg_allele2, sampled_covg_rest_of_genome);
update_allele(var->one_allele, var->len_one_allele,
colour_indiv, sampled_covg_allele1,read_len-kmer+1);
update_allele(var->other_allele, var->len_other_allele,
colour_indiv, sampled_covg_allele2, read_len-kmer+1);
//update_allele(genome_minus_site,len_genome_minus_site, colour_indiv, sampled_covg_rest_of_genome);
test(var, model_info, fasta, colour_ref_minus_site,
colour_indiv, using_1and2_nets,
working_colour1, working_colour2,
&count_passes, &count_fails, db_graph, true_ml_gt_name);
}
//cleanup
zero_allele(var->one_allele, var->len_one_allele, colour_indiv, colour_allele1, colour_allele2, colour_ref_minus_site);
zero_allele(var->other_allele, var->len_other_allele, colour_indiv, colour_allele1, colour_allele2, colour_ref_minus_site);
CU_ASSERT((double)count_passes/(double)(count_passes+count_fails) > 0.9 );//actually, we could set this to ==1
printf("Number of passes: %d, number of fails %d\n", count_passes, count_fails);
gsl_rng_free (r);
}
