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mecat2cns/mecat_correction.cpp fix #14

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mecat2cns/mecat_correction.cpp fix #14

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23 changes: 10 additions & 13 deletions src/mecat2cns/mecat_correction.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -160,33 +160,30 @@ output_cns_result(std::vector<CnsResult>& cns_results,
std::string& cns_seq)
{
const size_t MaxSeqSize = 60000;
const size_t BlkSize = 50000;
const size_t OvlpSize = 10000;
// BlkSize must be >= OvlpSize
const size_t BlkSize = MaxSeqSize - OvlpSize - 1000;

size_t size = cns_seq.size();
const size_t size = cns_seq.size();
if (size <= MaxSeqSize) {
cr.range[0] = beg;
cr.range[1] = end;
cr.seq = cns_seq;
cns_results.push_back(cr);
} else {
const size_t cutoff = size - OvlpSize - 1000;
size_t L = 0, R;
size_t left = size;
while (left) {
R = std::min(L + BlkSize, size);
size_t blksize = R - L;
left -= blksize;
if (left <= OvlpSize + 1000) {
do {
R = L + BlkSize;
if (R >= cutoff) {
R = size;
blksize += left;
left = 0;
}
cr.range[0] = L + beg;
cr.range[1] = R + beg;
cr.seq = cns_seq.substr(L, blksize);
cr.range[1] = R < size && R + beg < static_cast<size_t>(end) ? R + beg : end;
cr.seq = cns_seq.substr(L, R - L);
cns_results.push_back(cr);
L = R - OvlpSize;
}
} while (R < size);
}
}

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