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fix incremental build #584

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Merged
merged 1 commit into from
Nov 26, 2024
Merged

fix incremental build #584

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9 changes: 2 additions & 7 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,8 @@ ${BIN_TARGET}:${OBJ}
static:${OBJ}
$(CXX) $(OBJ) -o ${BIN_TARGET} $(STATIC_LD_FLAGS)

${DIR_OBJ}/%.o:${DIR_SRC}/%.cpp make_obj_dir
${DIR_OBJ}/%.o:${DIR_SRC}/%.cpp
@mkdir -p $(@D)
$(CXX) -c $< -o $@ $(CXXFLAGS)

.PHONY:clean
Expand All @@ -43,12 +44,6 @@ clean:
rm $(TARGET) ; \
fi

make_obj_dir:
@if test ! -d $(DIR_OBJ) ; \
then \
mkdir $(DIR_OBJ) ; \
fi

install:
install $(TARGET) $(BINDIR)/$(TARGET)
@echo "Installed."
2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -357,7 +357,7 @@ means that 150bp are from read1, and 15bp are from read2. `fastp` prefers the ba
Same as the [base correction feature](#base-correction-for-pe-data), this function is also based on overlapping detection, which has adjustable parameters `overlap_len_require (default 30)`, `overlap_diff_limit (default 5)` and `overlap_diff_percent_limit (default 20%)`. Please note that the reads should meet these three conditions simultaneously.

# duplication rate and deduplication
For both SE and PE data, fastp supports evaluating its duplication rate and removing duplicated reads/pairs. fastp considers one read as duplicated only if its all base pairs are identical as another one. This meas if there is a sequencing error or an N base, the read will not be treated as duplicated.
For both SE and PE data, fastp supports evaluating its duplication rate and removing duplicated reads/pairs. fastp considers one read as duplicated only if its all base pairs are identical as another one. This means if there is a sequencing error or an N base, the read will not be treated as duplicated.

## duplication rate evaluation
By default, fastp evaluates duplication rate, and this module may use 1G memory and take 10% ~ 20% more running time. If you don't need the duplication rate information, you can set `--dont_eval_duplication` to disable the duplication evaluation. But please be noted that, if deduplication (`--dedup`) option is enabled, then `--dont_eval_duplication` option is ignored.
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2 changes: 1 addition & 1 deletion src/peprocessor.cpp
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Expand Up @@ -360,7 +360,7 @@ void PairEndProcessor::recycleToPool2(int tid, Read* r) {
bool PairEndProcessor::processPairEnd(ReadPack* leftPack, ReadPack* rightPack, ThreadConfig* config){
if(leftPack->count != rightPack->count) {
cerr << endl;
cerr << "WARNNIG: different read numbers of the " << mPackProcessedCounter << " pack" << endl;
cerr << "WARNING: different read numbers of the " << mPackProcessedCounter << " pack" << endl;
cerr << "Read1 pack size: " << leftPack->count << endl;
cerr << "Read2 pack size: " << rightPack->count << endl;
cerr << endl;
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