<commit_before>class Kallisto < Formula
  desc "Quantify abundances of transcripts from RNA-Seq data"
  homepage "https://pachterlab.github.io/kallisto/"
  url "https://github.com/pachterlab/kallisto/archive/v0.46.1.tar.gz"
  sha256 "492ef081395e8858fcd9832aceb8b61c79358f00afb45e6709146c0fb51dd231"
  revision 1

  bottle do
    cellar :any
    sha256 "b4607b4f7c8ab90d206737c8373bdb23f30c2324e06312715562b6316aea7740" => :catalina
    sha256 "e11e83e697ca5c7854b2a8b981f5ab3fb24040b55d4e926aa33051ea792a72ce" => :mojave
    sha256 "afc1a45d8696b4c134a09098bac7641add23116f824f069e79ea9431f1267a37" => :high_sierra
  end

  depends_on "autoconf" => :build
  depends_on "automake" => :build
  depends_on "cmake" => :build
  depends_on "hdf5"

  def install
    # Upstream issue 15 Feb 2018 "cmake does not run autoreconf for htslib"
    # https://github.com/pachterlab/kallisto/issues/159
    system "autoreconf", "-fiv", "ext/htslib"

    system "cmake", ".", *std_cmake_args

    # Upstream issue 15 Feb 2018 "parallelized build failure"
    # https://github.com/pachterlab/kallisto/issues/160
    # Upstream issue 15 Feb 2018 "cannot use system htslib"
    # https://github.com/pachterlab/kallisto/issues/161
    system "make", "htslib"

    system "make", "install"
  end
<commit_msg>kallisto 0.46.2<commit_after>class Kallisto < Formula
  desc "Quantify abundances of transcripts from RNA-Seq data"
  homepage "https://pachterlab.github.io/kallisto/"
  url "https://github.com/pachterlab/kallisto/archive/v0.46.2.tar.gz"
  sha256 "c447ca8ddc40fcbd7d877d7c868bc8b72807aa8823a8a8d659e19bdd515baaf2"

  bottle do
    cellar :any
    sha256 "b4607b4f7c8ab90d206737c8373bdb23f30c2324e06312715562b6316aea7740" => :catalina
    sha256 "e11e83e697ca5c7854b2a8b981f5ab3fb24040b55d4e926aa33051ea792a72ce" => :mojave
    sha256 "afc1a45d8696b4c134a09098bac7641add23116f824f069e79ea9431f1267a37" => :high_sierra
  end

  depends_on "autoconf" => :build
  depends_on "automake" => :build
  depends_on "cmake" => :build
  depends_on "hdf5"

  def install
    # Upstream issue 15 Feb 2018 "cmake does not run autoreconf for htslib"
    # https://github.com/pachterlab/kallisto/issues/159
    system "autoreconf", "-fiv", "ext/htslib"

    system "cmake", ".", *std_cmake_args

    # Upstream issue 15 Feb 2018 "parallelized build failure"
    # https://github.com/pachterlab/kallisto/issues/160
    # Upstream issue 15 Feb 2018 "cannot use system htslib"
    # https://github.com/pachterlab/kallisto/issues/161
    system "make", "htslib"

    system "make", "install"
  end

{'fraction_non_alphanumeric': 0.10136452241715399, 'fraction_numerical': 0.16686159844054582, 'mean_word_length': 4.436440677966102, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 15, 'https://': 10, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3783147', 'n_tokens_mistral': 1296, 'n_tokens_neox': 1045, 'n_words': 185}