void
merge(istream &cpg_stream, ostream &dmr_stream, double cutoff) {
bool skipped_last_cpg, sig_raw;
GenomicRegion dmr;
dmr.set_name("dmr");
size_t dmr_test_cov = 0; size_t dmr_test_meth = 0;
size_t dmr_rest_cov = 0; size_t dmr_rest_meth = 0;
size_t test_cov = 0; size_t test_meth = 0;
size_t rest_cov = 0; size_t rest_meth = 0;
// Find the first significant CpG, or terminate the function if none exist.
if (!read_next_significant_cpg(cpg_stream, dmr, cutoff, skipped_last_cpg,
sig_raw, test_cov, test_meth, rest_cov, rest_meth))
return;
dmr.set_score(sig_raw);
dmr_test_cov += test_cov;
dmr_test_meth += test_meth;
dmr_rest_cov += rest_cov;
dmr_rest_meth += rest_meth;
GenomicRegion cpg;
cpg.set_name("dmr");
while(read_next_significant_cpg(cpg_stream, cpg, cutoff, skipped_last_cpg,
sig_raw, test_cov, test_meth, rest_cov, rest_meth)) {
if (skipped_last_cpg || cpg.get_chrom() != dmr.get_chrom()) {
if (dmr.get_score() != 0)
dmr_stream << dmr.get_chrom() << '\t'
<< dmr.get_start() << '\t'
<< dmr.get_end() << '\t'
<< dmr.get_name() << '\t'
<< dmr.get_score() << '\t'
<< double(dmr_test_meth)/dmr_test_cov -
double(dmr_rest_meth)/dmr_rest_cov << std::endl;
dmr = cpg;
dmr.set_score(sig_raw);
dmr_test_cov = test_cov;
dmr_test_meth = test_meth;
dmr_rest_cov = rest_cov;
dmr_rest_meth = rest_meth;
} else {
dmr.set_end(cpg.get_end());
dmr.set_score(dmr.get_score() + sig_raw);
dmr_test_cov += test_cov;
dmr_test_meth += test_meth;
dmr_rest_cov += rest_cov;
dmr_rest_meth += rest_meth;
}
}
dmr_stream << dmr << std::endl;
}
