<commit_before>class PicardTools < Formula
  desc "Tools for manipulating HTS data and formats"
  homepage "https://broadinstitute.github.io/picard/"
  url "https://github.com/broadinstitute/picard/releases/download/2.27.2/picard.jar"
  sha256 "f7b623a93a56efd54f8d93220650ec31f9159c7ec20e431be834cfb221c61a2e"
  license "MIT"

  livecheck do
    url :stable
    strategy :github_latest
  end

  bottle do
    sha256 cellar: :any_skip_relocation, all: "91603420700d2a3f9f9dd474dff2e9c593e15f6147efa7aa6acf40bd8200a16b"
  end

  depends_on "openjdk"

  def install
    libexec.install "picard.jar"
    (bin/"picard").write <<~EOS
      #!/bin/bash
      exec "#{Formula["openjdk"].opt_bin}/java" $JAVA_OPTS -jar "#{libexec}/picard.jar" "$@"
    EOS
  end

  test do
    (testpath/"test.fasta").write <<~EOS
      >U00096.2:1-70
      AGCTTTTCATTCTGACTGCAACGGGCAATATGTCT
      CTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
    EOS<commit_msg>picard-tools 2.27.3<commit_after>class PicardTools < Formula
  desc "Tools for manipulating HTS data and formats"
  homepage "https://broadinstitute.github.io/picard/"
  url "https://github.com/broadinstitute/picard/releases/download/2.27.3/picard.jar"
  sha256 "4b375ca3d1a82fbe0206fc9b363e7082a4fa14aff689f5e0e3311de5006a16c8"
  license "MIT"

  livecheck do
    url :stable
    strategy :github_latest
  end

  bottle do
    sha256 cellar: :any_skip_relocation, all: "91603420700d2a3f9f9dd474dff2e9c593e15f6147efa7aa6acf40bd8200a16b"
  end

  depends_on "openjdk"

  def install
    libexec.install "picard.jar"
    (bin/"picard").write <<~EOS
      #!/bin/bash
      exec "#{Formula["openjdk"].opt_bin}/java" $JAVA_OPTS -jar "#{libexec}/picard.jar" "$@"
    EOS
  end

  test do
    (testpath/"test.fasta").write <<~EOS
      >U00096.2:1-70
      AGCTTTTCATTCTGACTGCAACGGGCAATATGTCT
      CTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
    EOS
{'fraction_non_alphanumeric': 0.10771704180064309, 'fraction_numerical': 0.10664523043944266, 'mean_word_length': 3.952254641909814, 'pattern_counts': {'":': 0, '<': 13, '<?xml version=': 0, '>': 5, 'https://': 4, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 2, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4787078', 'n_tokens_mistral': 885, 'n_tokens_neox': 775, 'n_words': 116}