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/2.25.5/picard.jar"
  sha256 "f7fa9784b84d384abfcbd77076f5ceab7b2797dc863ac35fd41470daa3efe3a5"
  license "MIT"

  livecheck do
    url :stable
    strategy :github_latest
  end

  bottle do
    sha256 cellar: :any_skip_relocation, all: "bdaf5ca6f12440de58e1513ae29215c776978e33b4093c27daa346d18258068b"
  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
    cmd = "#{bin}/picard NormalizeFasta I=test.fasta O=/dev/stdout"
    assert_match "TCTCTG", shell_output(cmd)
  end
end