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fix duplication accuracy level calculations logic bug #649

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Merged
sfchen merged 1 commit into from
Jan 14, 2026
Merged

fix duplication accuracy level calculations logic bug #649

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6 changes: 3 additions & 3 deletions src/duplicate.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ Duplicate::Duplicate(Options* opt) {
// level 3: 4G
// level 4: 8G
// level 5: 16G
// level 6: 24G
// level 6: 32G
switch(mOptions->duplicate.accuracyLevel) {
case 1:
break;
Expand All @@ -40,7 +40,7 @@ Duplicate::Duplicate(Options* opt) {
break;
case 6:
mBufLenInBytes *= 8;
mBufNum *= 3;
mBufNum *= 4;
break;
default:
break;
Expand Down Expand Up @@ -161,7 +161,7 @@ bool Duplicate::applyBloomFilter(uint64* positions) {

//isDup = isDup && (mDupBuf[i * mBufLenInBytes + bytePos] & byte);
uint8 ret = atomic_fetch_or(mDupBuf + i * mBufLenInBytes + bytePos, byte);
isDup = (ret & byte) != 0;
isDup &= (ret & byte) != 0;
}
return isDup;
}
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2 changes: 1 addition & 1 deletion src/main.cpp
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Expand Up @@ -70,7 +70,7 @@ int main(int argc, char* argv[]){

// duplication evaluation and deduplication
cmd.add("dedup", 'D', "enable deduplication to drop the duplicated reads/pairs");
cmd.add<int>("dup_calc_accuracy", 0, "accuracy level to calculate duplication (1~6), higher level uses more memory (1G, 2G, 4G, 8G, 16G, 24G). Default 1 for no-dedup mode, and 3 for dedup mode.", false);
cmd.add<int>("dup_calc_accuracy", 0, "accuracy level to calculate duplication (1~6), higher level uses more memory (1G, 2G, 4G, 8G, 16G, 32G). Default 1 for no-dedup mode, and 3 for dedup mode.", false);
cmd.add("dont_eval_duplication", 0, "don't evaluate duplication rate to save time and use less memory.");

// polyG tail trimming
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