static void readPairs(It& it, const It& last, vector<SAMRecord>& out)
{
assert(out.empty());
for (; it != last; ++it) {
if (it->isUnmapped() || it->isMateUnmapped()
|| !it->isPaired() || it->rname == it->mrnm
|| it->mapq < opt::minMapQ)
continue;
if (!out.empty() && out.back().rname != it->rname)
break;
out.push_back(*it);
SAMRecord& sam = out.back();
// Clear unused fields.
sam.qname.clear();
#if SAM_SEQ_QUAL
sam.seq.clear();
sam.qual.clear();
#endif
}
// Check that the input is sorted.
if (it != last && !out.empty()
&& get(g_contigNames, it->rname)
< get(g_contigNames, out.front().rname)) {
cerr << "error: input must be sorted: saw `"
<< out.front().rname << "' before `"
<< it->rname << "'\n";
exit(EXIT_FAILURE);
}
}
