rlpbwt

Other run-length encoded PBWT implementations can be found at koeppl/pbwt.

Type of RLPBWT

In this repository we have various possible versions of RLPBWT:

• rlpbwt_naive
• rlpbwt_bv (practically the previous one with bitvectors for runs and u/v values)
• rlpbwt_ms with the panel as bitvectors
• rlpbwt_ms with the panel as an SLP (for random access or LCE query)

The first two can be queried to obtain the number of rows that are matching at column k while the last two (if extended with the phi data structure) could also report the exact rows that are matching.

Build

to build:

cmake -S . -B build -D BUILD_TESTS=OFF
cmake --build build

to execute:

cd build
./rlpbwr [options]

usage:

Usage: RLPBWT [options]

Options:
  -i, --input_file <path>	 macs file for panel
  -m, --memorize <path>	  path to save serialization 
  -l, --load <path>	 path to load serialization
  -s, --input_slp <path>	 path to SLP file
  -o, --output <path>	 path to query output
  -q, --query <path>	 path to macs query file
  -N, --Naive	 naive RLPBWT (only one mode allowed)
  -B, --Bv	 bitvectors RLPBWT (only one mode allowed)
  -S, --Slp	 slp RLPBWT (only one mode allowed | slp file required)
  -P, --Panel	 panel RLPBWT (only one mode allowed)
  -t, --thresholds	 enable thresholds (slp/panel mode only)
  -e, --extend	 extend matches (slp/panel mode only)
  -r, --raw	use compressed intvectors instead of sparse bitvectors
  -v, --verbose	 extra prints
  -V, --fverbose	 extra prints for functions (cautions)
  -h, --help	 show this help message and exit

example using RLPBWT (slp mode) with lce queries and matches extended:

./rlpbwt -i <input matrix> -s <slp file> -o <output file> -q <query file> -S -e

Test

to build tests:

cmake -S . -B build_test -D BUILD_TESTS=ON
cmake --build build_test

to execute:

mkdir output
cd build_test
./rlpbwt_test