Sampled and Parallel Positional Burrows-Wheeler Transform

Install

export LIBOMP=/path/to/lib
export HTSLIB=/path/to/lib
git clone https://github.com/msgr0/sp-pbwt.git
cd sp-pbwt
make

BCF input:

Run ./sp-pbwt-bcf MODE FILE, with one of the available modes:

Syscall:

• linear
• sampled
• blockpar
• stagpar

BM input:

Run ./sp-pbwt-bm MODE FILE, with one of the available modes:

Syscall:

• linear-syscall
• sampled-syscall
• blockpar-syscall
• stagpar-syscall

Memory Mapping:

• linear-mmap
• sampled-mmap
• blockpar-mmap
• stagpar-mmap