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Always call next() on both tokenizers, to make sure both r1 and r2 files are read to the end #53

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Always call next() on both tokenizers, to make sure both r1 and r2 files are read to the end #53

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18 changes: 16 additions & 2 deletions src/lib/workflow/DualFastq2SamWorkflow.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,14 @@ align::InsertSizeParameters DualFastq2SamWorkflow::requestInsertSizeInfo(

align::InsertSizeParameters ret;
bool retDone = false;
while (r1Tokenizer.next() && r2Tokenizer.next()) {
while (true) {
// Always call next() on both tokenizers, to make sure both files are read to the end.
const bool r1Next = r1Tokenizer.next();
const bool r2Next = r2Tokenizer.next();
if (!r1Next || !r2Next) {
break;
}

const auto& r1Token = r1Tokenizer.token();
const auto& r2Token = r2Tokenizer.token();
// std::cout << "token: " << r1Token << "-" << r2Token << "\n";
Expand Down Expand Up @@ -89,7 +96,14 @@ void DualFastq2SamWorkflow::alignDualFastq(
align::Aligner::ReadPair pair;

int64_t fragmentId = 0;
while (r1Tokenizer.next() && r2Tokenizer.next()) {
while (true) {
// Always call next() on both tokenizers, to make sure both files are read to the end.
const bool r1Next = r1Tokenizer.next();
const bool r2Next = r2Tokenizer.next();
if (!r1Next || !r2Next) {
break;
}

const auto& r1Token = r1Tokenizer.token();
const auto& r2Token = r2Tokenizer.token();
// std::cout << "token: " << r1Token << "-" << r2Token << "\n";
Expand Down