// Attemps to find the next significant CpG site. Returns true if one was found
// and flase otherwise.
static bool
read_next_significant_cpg(istream &cpg_stream, GenomicRegion &cpg,
double cutoff, bool &skipped_any, bool &sig_raw,
size_t &test_cov, size_t &test_meth,
size_t &rest_cov, size_t &rest_meth) {
GenomicRegion region;
skipped_any = false;
sig_raw = false;
string cpg_encoding;
while (getline(cpg_stream, cpg_encoding)) {
string record, chrom, name, sign;
size_t position;
double raw_pval, adjusted_pval, corrected_pval;
std::istringstream iss(cpg_encoding);
iss.exceptions(std::ios::failbit);
iss >> chrom >> position >> sign >> name >> raw_pval
>> adjusted_pval >> corrected_pval
>> test_cov >> test_meth >> rest_cov >> rest_meth;
if (0 <= corrected_pval && corrected_pval < cutoff) {
cpg.set_chrom(chrom);
cpg.set_start(position);
cpg.set_end(position + 1);
sig_raw = (0 <= raw_pval && raw_pval < cutoff);
return true;
}
skipped_any = true;
}
return false;
}
static void
get_chrom(const MappedRead &mr,
const chrom_file_map &chrom_files,
GenomicRegion &chrom_region, string &chrom) {
const chrom_file_map::const_iterator fn(chrom_files.find(mr.r.get_chrom()));
if (fn == chrom_files.end())
throw SMITHLABException("could not find chrom: " + mr.r.get_chrom());
chrom.clear();
read_fasta_file(fn->second, mr.r.get_chrom(), chrom);
if (chrom.empty())
throw SMITHLABException("could not find chrom: " + mr.r.get_chrom());
chrom_region.set_chrom(mr.r.get_chrom());
}
static void
get_chrom(const bool VERBOSE, const GenomicRegion &r,
const unordered_map<string, string>& chrom_files,
GenomicRegion &chrom_region, string &chrom) {
const unordered_map<string, string>::const_iterator
fn(chrom_files.find(r.get_chrom()));
if (fn == chrom_files.end())
throw runtime_error("could not find chrom: " + r.get_chrom());
chrom.clear();
read_fasta_file(fn->second, r.get_chrom(), chrom);
if (chrom.empty())
throw runtime_error("could not find chrom: " + r.get_chrom());
else {
chrom_region.set_chrom(r.get_chrom());
}
}
static void
get_chrom(const MappedRead &mr,
const vector<string> &all_chroms,
const unordered_map<string, size_t> &chrom_lookup,
GenomicRegion &chrom_region, string &chrom) {
const unordered_map<string, size_t>::const_iterator
the_chrom(chrom_lookup.find(mr.r.get_chrom()));
if (the_chrom == chrom_lookup.end())
throw runtime_error("could not find chrom: " + mr.r.get_chrom());
chrom = all_chroms[the_chrom->second];
if (chrom.empty())
throw runtime_error("could not find chrom: " + mr.r.get_chrom());
chrom_region.set_chrom(mr.r.get_chrom());
}
