<commit_before>class Bcftools < Formula
  desc "Tools for BCF/VCF files and variant calling from samtools"
  homepage "https://www.htslib.org/"
  url "https://github.com/samtools/bcftools/releases/download/1.11/bcftools-1.11.tar.bz2"
  sha256 "3ceee47456ec481f34fa6c34beb6fe892b5b365933191132721fdf126e45a064"
  license "MIT"

  livecheck do
    url :stable
    strategy :github_latest
  end

  bottle do
    sha256 arm64_big_sur: "59762e9109882da66c1ebf0d0381f5d38cada1e58732025f0c91ab9cb85f0031"
    sha256 big_sur:       "67d1219c5df4b512f08199740257e15b38422ba461c2de3ef2ed0697c8e28305"
    sha256 catalina:      "fb3b25ef0fa059b400d4094e9719208c74b7665c45d378aec46f26efe5c179c6"
    sha256 mojave:        "cbc6f8a457ddb9d4e6c14a1b5f78023f66305aa9df7f8495252b9a774821fec9"
    sha256 high_sierra:   "d6ea207bfe680f637147e39e7cf2f3311709dc3c1964bdf5d3506d13200da7a8"
  end

  depends_on "gsl"
  depends_on "htslib"
  depends_on "xz"

  def install
    system "./configure", "--prefix=#{prefix}",
                          "--with-htslib=#{Formula["htslib"].opt_prefix}",
                          "--enable-libgsl"
    system "make", "install"
    pkgshare.install "test/query.vcf"
  end

  test do
    output = shell_output("#{bin}/bcftools stats #{pkgshare}/query.vcf")
    assert_match "number of SNPs:\t3", output
    assert_match "fixploidy", shell_output("#{bin}/bcftools plugin -l")
  end
end<commit_msg>bcftools 1.12 (also remove extra depends_on and fix license)<commit_after>class Bcftools < Formula
  desc "Tools for BCF/VCF files and variant calling from samtools"
  homepage "https://www.htslib.org/"
  url "https://github.com/samtools/bcftools/releases/download/1.12/bcftools-1.12.tar.bz2"
  sha256 "7a0e6532b1495b9254e38c6698d955e5176c1ee08b760dfea2235ee161a024f5"
  # The bcftools source code is MIT/Expat-licensed, but when it is configured
  # with --enable-libgsl the resulting executable is GPL-licensed.
  license "GPL-3.0-or-later"

  livecheck do
    url :stable
    strategy :github_latest
  end

  bottle do
    sha256 arm64_big_sur: "59762e9109882da66c1ebf0d0381f5d38cada1e58732025f0c91ab9cb85f0031"
    sha256 big_sur:       "67d1219c5df4b512f08199740257e15b38422ba461c2de3ef2ed0697c8e28305"
    sha256 catalina:      "fb3b25ef0fa059b400d4094e9719208c74b7665c45d378aec46f26efe5c179c6"
    sha256 mojave:        "cbc6f8a457ddb9d4e6c14a1b5f78023f66305aa9df7f8495252b9a774821fec9"
    sha256 high_sierra:   "d6ea207bfe680f637147e39e7cf2f3311709dc3c1964bdf5d3506d13200da7a8"
  end

  depends_on "gsl"
  depends_on "htslib"

  def install
    system "./configure", "--prefix=#{prefix}",
                          "--with-htslib=#{Formula["htslib"].opt_prefix}",
                          "--enable-libgsl"
    system "make", "install"
    pkgshare.install "test/query.vcf"
  end

  test do
    output = shell_output("#{bin}/bcftools stats #{pkgshare}/query.vcf")
    assert_match "number of SNPs:\t3", output
    assert_match "fixploidy", shell_output("#{bin}/bcftools plugin -l")
  end
end
{'fraction_non_alphanumeric': 0.09386401326699834, 'fraction_numerical': 0.18673300165837478, 'mean_word_length': 3.9361702127659575, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 3, 'https://': 4, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, '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': '7443442', 'n_tokens_mistral': 1527, 'n_tokens_neox': 1233, 'n_words': 189}