anantkm/BWT

Your task in this assignment is to create two programs: a search program called bwtsearch that implements BWT backward search, which can efficiently search a BWT encoded DNA file; and a decoder program called bwtdecode that efficiently decodes BWT encoded DNA file back to its original DNA sequence

BWT Encoder/Decoder

This project provides two command line programs for Burrows-Wheeler transform (BWT) encoding and decoding of text files:

• bwtsearch: searches for a given pattern in the BWT encoded file
• bwtdecode: decodes a BWT encoded file back to its original format

Getting Started

Prerequisites

The project requires the following software to be installed on the system:

• GCC (GNU Compiler Collection) for compiling the C code

Building the Programs

To build the programs, navigate to the project directory and run the following command:

make

This will compile both the bwtsearch and bwtdecode programs and create the executable files in the same directory.

Running the Programs

bwtsearch

To search for a pattern in a BWT encoded file, run the following command:

./bwtsearch

This will output the positions of the pattern in the original file.

bwtdecode

To decode a BWT encoded file, run the following command:

./bwtdecode