class Fgbio < Formula
  desc "Tools for working with genomic and high throughput sequencing data"
  homepage "https://fulcrumgenomics.github.io/fgbio/"
  url "https://github.com/fulcrumgenomics/fgbio/releases/download/2.1.0/fgbio-2.1.0.jar"
  sha256 "7a07d86b1263a89375c5796fec51ecc4bf31b3850ec205df8ae8c9ccba7ca314"
  license "MIT"

  bottle do
    sha256 cellar: :any_skip_relocation, all: "7c81e532d95c24a74ec06c7999cc471ee4c4b7386bacc6f2e04f6d49b466de61"
  end

  depends_on "openjdk"

  def install
    libexec.install "fgbio-#{version}.jar"
    bin.write_jar_script libexec/"fgbio-#{version}.jar", "fgbio"
  end

  test do
    (testpath/"test.fasta").write <<~EOS
      >U00096.2:1-70
      AGCTTTTCATTCTGACTGCAACGGGCAATATGTCT
      ctgtgtggattaaaaaaagagtgtctgatagcagc
    EOS
    cmd = "#{bin}/fgbio HardMaskFasta -i test.fasta -o /dev/stdout"
    assert_match "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN", shell_output(cmd)
  end
end