RLZAP

This project is an implementation of the compressed relative index strategy outlined in the paper "RLZAP: Relative Lempel-Ziv with Adaptive Pointers". The dataset used for the experiments is available here

Compiling

To compile it:

git clone https://github.com/farruggia/rlzap
mkdir rlzap/build
cd rlzap/build
cmake ..
make

The project is written in C++11, so a "modern" compiler is required. No external dependency is required (unless additional options are requested - see section "Advanced usage")

Usage

Relatively compress DNA file input against reference, using the RLZAP strategy, into input_index:

./rlzap_build input reference input.rlz

To use the RLZ strategy instead:

./rlz_build input reference input.rlz

To decompress input_index back into input (regardless of the compression strategy used):

./index_decompress input.rlzap reference input

To display characters ranging from the 50th to the 100th:

./index_extract input.rlzap reference 50 100

To relatively compress DLCP files instead, just use the -A option:

./index_build dlcp_input dlcp_reference dlcp_input.rlzap -A dlcp32

Compression/representation parameters (like DeltaBits or MaxLiteral) can be tuned by using the appropriate command-line options of index_build: just invoke the tool without any argument to show all the options.

Advanced usage

Using the project as a library

All the functionalities provided by this project are exposed through an API. Consult the header file include/rlz/api.hpp for the list of supported functions, or have a look at the files into the example directory for some examples on invoking the functions and successfully compile and link against RLZAP as a third-party library.

Compilation options

The CMakeLists defines a list of build options:

• RLZ_BINARIES: enables or disables generating the binaries. By default, this is OFF, and only the library is built. Turn it ON to build the binaries as well.
• RLZ_BENCHMARK: if RLZ_BINARIES is ON, builds the benchmark utility. Needs libPAPI as an external library.
• RLZ_TESTS: builds the unit tests.
• RLZ_USE_EXTERNAL_SDSL: use external SDSL library found using pkg-config. ON by default, set OFF to use the SDSL shipped as a submodule.