<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/2.24.1/picard.jar"
  sha256 "69c0ac607c99df9f2162a6b685a3b147e83a1501ad2be86cb587cb06f1cbc11f"
  license "MIT"

  livecheck do
    url :stable
    strategy :github_latest
  end

  bottle :unneeded

  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<commit_msg>picard-tools 2.24.2 (#70314)<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/2.24.2/picard.jar"
  sha256 "3be6c0eef3fb63d01b140fa712313a3b58b40dc01654b3b61aec349edab9e6ce"
  license "MIT"

  livecheck do
    url :stable
    strategy :github_latest
  end

  bottle :unneeded

  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
{'fraction_non_alphanumeric': 0.11865443425076452, 'fraction_numerical': 0.06972477064220184, 'mean_word_length': 3.755813953488372, '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': '4589620', 'n_tokens_mistral': 723, 'n_tokens_neox': 648, 'n_words': 103}