<commit_before>class Ropebwt2 < Formula
  homepage "https://github.com/lh3/ropebwt2"
  head "https://github.com/lh3/ropebwt2.git"
  # pdf "http://arxiv.org/pdf/1406.0426v1.pdf"

  url "https://github.com/lh3/ropebwt2/archive/49b280debe54db51d9ca81972a9db76c2f6290f7.tar.gz"
  version "r181"
  sha256 "bcd762ea63d907a52efd573b944ca2d3d1338d1f814ad855124d450916e0d75a"

  def install
    system "make"
    bin.install "ropebwt2"
    doc.install "README.md", "tex/ropebwt2.tex"
  end

  test do
    system "ropebwt2 2>&1 |grep -q ropebwt2"<commit_msg>ropebwt2: Add desc, doi and tag bioinformatics<commit_after>class Ropebwt2 < Formula
  desc "Incremental construction of FM-index for DNA sequences"
  homepage "https://github.com/lh3/ropebwt2"
  url "https://github.com/lh3/ropebwt2/archive/49b280debe54db51d9ca81972a9db76c2f6290f7.tar.gz"
  version "r181"
  sha256 "bcd762ea63d907a52efd573b944ca2d3d1338d1f814ad855124d450916e0d75a"
  head "https://github.com/lh3/ropebwt2.git"
  # doi "10.1093/bioinformatics/btu541"
  # tag "bioinformatics"

  def install
    system "make"
    bin.install "ropebwt2"
    doc.install "README.md", "tex/ropebwt2.tex"
  end

  test do
    assert_match "Usage", shell_output("#{bin}/ropebwt2 2>&1", 1)
{'fraction_non_alphanumeric': 0.11941510966693746, 'fraction_numerical': 0.15190901705930138, 'mean_word_length': 4.475555555555555, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 6, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6736023', 'n_tokens_mistral': 649, 'n_tokens_neox': 549, 'n_words': 80}