diff-bench-paper

June 26, 2021 ยท View on GitHub

Edits to the supplementary data of the difference recurrence alignment paper.

The original paper by Hajime Suzuki and Masahiro Kasahara is here.

This repo exists because diffbench did not contain the exact code for the benchmarks in the paper. I needed to modify this code to compare against block aligner. These small modifications are my only contributions to this code. The initial code and paper are all by Suzuki and Kasahara.

Getting the data

sequences.txt is needed for the benchmarks to run. It is large, so it has to be manually downloaded:

  1. cd supplementary_data
  2. curl -OL https://github.com/Daniel-Liu-c0deb0t/diff-bench-paper/releases/download/v1.0/sequences.txt.gz
  3. gunzip sequences.txt.gz
  4. cd ..

Building and running

  1. cd supplementary_data/benchmark_codes
  2. Check the Makefile to make sure it is using the right gcc versions.
  3. Run ./custom_bench.sh to benchmark and print results.
  4. Run ./custom_scores.sh to output scores as tab-separated files, for comparison against block aligner.