KFC

kmer week experiment

Building

Prior to any compilation, please check your gcc version. It must be 8+.

To build a debug version (default in this early development stage):

git clone https://github.com/Malfoy/KFC.git
cd KFC
make -j

For an optimized build add DEBUG=0 to the make command:

make -j DEBUG=0

For building with optimizations while keeping asserts enabled, use make -j DEBUG=0 ASSERTS=1

If you have clang-format installed on your system, please setup the pre-commit hook:

.scripts/install_hooks.sh

Please use the snakefile to compare latest KMC version with KFC.

snakemake --config color="blue"
snakemake --config color="red"

Name		Name	Last commit message	Last commit date
Latest commit History 211 Commits
data		data
dsk_phases		dsk_phases
scripts		scripts
tests		tests
thirdparty		thirdparty
.clang-format		.clang-format
.gitattributes		.gitattributes
.gitignore		.gitignore
.gitmodules		.gitmodules
.travis.yml		.travis.yml
BitSet.cpp		BitSet.cpp
BitSet.hpp		BitSet.hpp
BloomFilter.cpp		BloomFilter.cpp
BloomFilter.hpp		BloomFilter.hpp
CascadingBloomFilter.cpp		CascadingBloomFilter.cpp
CascadingBloomFilter.hpp		CascadingBloomFilter.hpp
DenseMenu.hpp		DenseMenu.hpp
DenseMenuYo.hpp		DenseMenuYo.hpp
Hash.cpp		Hash.cpp
Hash.hpp		Hash.hpp
Kmers.cpp		Kmers.cpp
Kmers.hpp		Kmers.hpp
README.md		README.md
SKC_tests.cpp		SKC_tests.cpp
Snakefile		Snakefile
SolidSampler.cpp		SolidSampler.cpp
SolidSampler.hpp		SolidSampler.hpp
SparseMenu.hpp		SparseMenu.hpp
SuperKmerCount.cpp		SuperKmerCount.cpp
SuperKmerCount.hpp		SuperKmerCount.hpp
SuperKmerLight.cpp		SuperKmerLight.cpp
SuperKmerLight.hpp		SuperKmerLight.hpp
bbhash.h		bbhash.h
blocked.hpp		blocked.hpp
buckets.cpp		buckets.cpp
buckets.hpp		buckets.hpp
evaluator.cpp		evaluator.cpp
kfc_blue.cpp		kfc_blue.cpp
kfc_red.cpp		kfc_red.cpp
kfc_red_fire.cpp		kfc_red_fire.cpp
makefile		makefile
pow2.hpp		pow2.hpp
sparse_growth_policy.h		sparse_growth_policy.h
sparse_hash.h		sparse_hash.h
sparse_map.h		sparse_map.h
strict_fstream.hpp		strict_fstream.hpp
utils.cpp		utils.cpp
zstr.hpp		zstr.hpp