version 0.1 (20240320)
version 0.2 (20241223)
ToDO: optimize code structure, add friendly comments

Effloc is an efficient locating algorithm for mass-occurrence biological patterns with FM-Index.

Effloc consists of three components, index building, pattern generating, and pattern locating. You should first build the FM-Index with the reference genome, and then perform the locating process.

1. Download (or clone) the source code form https://github.com/Lilu-guo/Effloc
2. Compile the source code.

   cd ./Effloc   
   make

1. Run the shell command:

   ./effloc <Follow the prompts to enter the genome file name>

1. Run the shell command:

   ./effloc <Follow the prompts to enter the pattern set name>

1. Run the shell command:

   ./effloc <Follow the prompts to enter the pattern set name and index file name>

Please report bugs to Email: guolilu@stu.xidian.edu.cn or jgxygll@163.com if any questions or suggestions.
Your feedback and test results are welcome.

Effloc is available under the MIT license.