HRCM Bioinformatics 1 project

This is a project from the course of Bioinformatics 1 in the Faculty of Electrical Engineering and Computing (FER).
The goal of this project is to implement the Hybrid Referential Compression Method based on the original article. The repository for the original article can be found here.
Testing results of our implementation can be found in the documentation file.

Authors:

Paulo Erak
Lara Grgurić

Compile

You can find and download the source code here.

System requirements:

GNU Make
7zip

Compiling:

Run 'make' in the source directory

Usage:

Compression:
compress.exe -r {ref_file_path} -f {tbc_file_path}*

• -r is the reference, {ref_file_path} is the path to the reference file, required
  
• -f is the to-be-compressed file, multiple {tbc_file_path} paths can be set, required at least one to-be-compressed file
  

Decompression:
7z e output.7a -y
decompress.exe {ref_file_path} output.fa

• {ref_file_path} is the path to the reference file, required
  

Example:

Compression of files e_coli_103_2.fa, e_coli_103_3.fa and e_coli_103_4.fa with e_coli_103_1.fa as reference file:
compress.exe -r e_coli_103_1.fa -f e_coli_103_2.fa e_coli_103_3.fa e_coli_103_4.fa

Decompression of files e_coli_103_2.fa, e_coli_103_3.fa and e_coli_103_4.fa with e_coli_103_1.fa as reference file:
7z e output.7a -y
decompress.exe e_coli_103_1.fa output.fa