git clone https://github.com/pg-space/fcgr.git
cd fcgr
mkdir build ; cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make
cd ..
fcgr takes as input the list of KMC databases (prefix used while running KMC).
For each of them, it outputs the FCGR in .npy format.
./fcgr [-m MASK] <in-kmc-list>
MASK is a bit string indicating which bases of a kmer to keep. For instance, if MASK=10011 and kmer is AACGT, kmer AGT will be stored in the FCGR. By default it's a k-long string of 1s.
Note: if input kmers are in canonical form, masked kmers won't be in canonical form anymore.
cd example
KMC=../build/kmc-prefix/src/kmc/bin/kmc
for fa in *.fa ; do $KMC -v -m4 -sm -b -ci0 -cs65535 -k6 -fm $fa $fa . ; done
ls $PWD/*.fa > list
../fcgr list
ls *.npy # <- these are the FCGR