diff --git a/Makefile b/Makefile index 2c8163f..2a0f833 100644 --- a/Makefile +++ b/Makefile @@ -1,9 +1,10 @@ .PHONY: all clean test cpptest verify quick-verify CXX= g++ -CXXFLAGS= -g -Wall -Wno-unused-function -std=c++17 -O2 +CXXFLAGS= -g -Wall -Wno-unused-function -std=c++17 -O3 LDFLAGS= -lz -lpthread SRC= src +UINT256= $(SRC)/uint256_t SCRIPTS= scripts DATA= data TESTS= tests @@ -24,13 +25,13 @@ verify: $(PROG) $(SCRIPTS)/verify.py $(DATA)/spneumoniae.fa quick-verify: $(PROG) $(SCRIPTS)/verify.py $(DATA)/spneumoniae.fa python $(SCRIPTS)/verify.py $(DATA)/spneumoniae.fa --quick --interpath $(DATA)/spyogenes.fa -$(PROG): $(SRC)/main.cpp $(SRC)/$(wildcard *.cpp *.h *.hpp) src/version.h +$(PROG): $(SRC)/main.cpp $(SRC)/$(wildcard *.cpp *.h *.hpp) src/version.h $(wildcard $(UINT256)/*.cpp $(UINT256)/*.h $(UINT256)/*.include) ./create-version.sh $(CXX) $(CXXFLAGS) $(SRC)/main.cpp $(SRC)/kthread.c -o $@ $(LDFLAGS) prophasmtest: $(TESTS)/unittest.cpp gtest-all.o $(SRC)/$(wildcard *.cpp *.h *.hpp) $(TESTS)/$(wildcard *.cpp *.h *.hpp) - $(CXX) $(CXXFLAGS) -isystem $(GTEST)/include -I $(GTEST)/include $(TESTS)/unittest.cpp gtest-all.o -pthread -o $@ $(LDFLAGS) + $(CXX) $(CXXFLAGS) -isystem $(GTEST)/include -I $(GTEST)/include $(TESTS)/unittest.cpp gtest-all.o -pthread -o $@ $(LDFLAGS) gtest-all.o: $(GTEST)/src/gtest-all.cc $(wildcard *.cpp *.h *.hpp) $(CXX) $(CXXFLAGS) -isystem $(GTEST)/include -I $(GTEST)/include -I $(GTEST) -DGTEST_CREATE_SHARED_LIBRARY=1 -c -pthread $(GTEST)/src/gtest-all.cc -o $@ diff --git a/README.md b/README.md index 73fdd41..2ea85c7 100644 --- a/README.md +++ b/README.md @@ -21,7 +21,7 @@ ProphAsm2 is a versatile tool for computing simplitigs/SPSS from *k-mer sets* and for *k-mer set operations*. The new features compared to the original [ProphAsm](https://github.com/prophyle/prophasm) include a largely speed and memory optimization, parallelization, -support for k-mer sizes up to 64 and support for minimum abundances. +support for k-mer sizes up to 128 and support for minimum abundances. Various types of sequencing datasets can be used as the input for ProphAsm, including genomes, pan-genomes, metagenomes or sequencing reads. @@ -74,8 +74,19 @@ Set operations: USAGE-BEGIN --> ``` - - +Usage: prophasm2 [options] +Command-line parameters: + -k INT K-mer size. + -i FILE Input FASTA file (can be used multiple times). + -o FILE Output FASTA file (if used, must be used as many times as -i). + -x FILE Compute intersection, subtract it, save it. + -s FILE Output file with k-mer statistics. + -t INT Number of threads (default 1). + -m INT Minimum abundance of k-mers to appear in the assembly (default 1). + -S Silent mode. + -u Do not consider k-mer and its reverse complement as equivalent. + +Note that '-' can be used for standard input/output. ```