We use cmake (version 3 or higher) for fastq_pair. The best way to install it is to use these commands:
mkdir build && cd build
cmake3 ../
make && sudo make install
If you don't have root access, you can also install fastq_pair in your home directory like this.
mkdir build && cd build
cmake3 -DCMAKE_INSTALL_PREFIX=$HOME/bin ..
make && make install
You should then be able to call `fastq_pair.
As noted in issue #3 you don't really need to use CMAKE at all.
As an alternative, you can run
gcc -std=gnu99 -o fastq_pair fastq_pair.c main.c robstr.c is_gzipped.c
Which will compile the code and create an executable for you!
This implementation is based on a hash table. The key factor that controls the speed of the program is the size of the table. We start with a default table size of 100,003. There are lots of recommendations on the table size, but for optimum speed it should approach (but doesn't have to be) the number of sequences in your fastq files.
You can alter the size of the table with the -t parameter. If you request a table that is too big for your available memory the program won't run.