README

System requirements:
- A 64-bit CPU
- The compilers gcc and a recent enough g++ with a support for the -std=c++11 flag

How to compile:

1. Load submodules:
  git submodule init
  git submodule update
2. Compile dependencies: Run the command "make dependencies" in the project root
   and hope for the best.
3. Compile the main project: Run the command "make release"

The final binary will be generated into the ./bin directory

The program is used as follows:
./bin/BWT_cluster --input-reads reads.fna

The program reads the configuration parameters from config.txt.
The config.txt contains the path of the eventual output file,
and parameters relating to the function the pipeline.
To override the default parameters, you can give them as command
line parameters like this:

./bin/BWT_cluster --input-reads reads.fna --preclustering-k 40 --threads 16

For a full list of available parameters see config.txt

You can also give your own config file with the --config option:
./bin/BWT_cluster --input-reads reads.fna --config my_config.txt

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For a clean stand-alone implementation of the BWT index used 
in this project, see github.com/jnalanko/BD_BWT_index