Implementing PBWT

This is my implementation of algorithm 1-4 from Richard Durbin's Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT) paper.

project structure

positional-burrows-wheeler-transform/
│
├── include/
│   └── pbwt.h                   # header file for PBWT class and function declarations
│
├── src/
│   ├── main.cpp                 # entry point
│   ├── pbwt_algos.cpp           # implementation of algorithms 1-4 (Separate mode)
│   ├── pbwt_algos_single_sweep.cpp # implementation of algorithms 1-4 (Single Sweep mode)
│   ├── utils.cpp                # utility functions
│
├── makefile                    
└── readme.md                   

run the code

build

git clone https://github.com/sajontahsen/positional-burrows-wheeler-transform.git
cd positional-burrows-wheeler-transform
mkdir build
make

run algorithms on separate mode (default)

./build/pbwt

run algorithms on single-sweep mode

./build/pbwt single 

console output

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PRs and suggestions are always welcome!