class Bwa < Formula
  desc "Burrow-Wheeler Aligner for pairwise alignment of DNA"
  homepage "https://github.com/lh3/bwa"
  url "https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2"
  sha256 "de1b4d4e745c0b7fc3e107b5155a51ac063011d33a5d82696331ecf4bed8d0fd"

  bottle do
    cellar :any_skip_relocation
    sha256 "6b07cef5ea1955d8a83e7b59ef8458a7604998f735f0eab85889fa3aedc7e953" => :mojave
    sha256 "02da3eecd6569c193a55436f705c8d351d052e44b79a43d6afc50f7308603a73" => :high_sierra
    sha256 "4db97125930b495fc34b6d161bea57171ac4bf2a5bf48ca1088a69a594874710" => :sierra
    sha256 "bee09d138e9d8f45c12d6c99b48a3e6891b6e4d3f5c6a6847bfeaa28afc2f362" => :el_capitan
  end

  def install
    system "make"

    # "make install" requested 26 Dec 2017 https://github.com/lh3/bwa/issues/172
    bin.install "bwa"
    man1.install "bwa.1"
  end

  test do
    (testpath/"test.fasta").write ">0\nAGATGTGCTG\n"
    system bin/"bwa", "index", "test.fasta"
    assert_predicate testpath/"test.fasta.bwt", :exist?
    assert_match "AGATGTGCTG", shell_output("#{bin}/bwa mem test.fasta test.fasta")
  end
end