<commit_before>require 'formula'

class Blasr < Formula
  homepage 'https://github.com/PacificBiosciences/blasr'
  #doi '10.1186/1471-2105-13-238'
  url 'https://github.com/PacificBiosciences/blasr/archive/smrtanalysis-2.1.tar.gz'
  sha1 'ac6add1ba8a82cac2515da36c0ec53060c20ea0f'
  head 'https://github.com/PacificBiosciences/blasr.git'

  depends_on "hdf5"

  fails_with :clang do
    build 503
    cause <<-EOS.undent
      error: destructor type 'HDFWriteBuffer<int>' in object
      destruction expression does not match the type
      'BufferedHDFArray<int>' of the object being destroyed
    EOS
  end

  fails_with :gcc do
    build 5666
    cause <<-EOS.undent
      error: invalid conversion
      from 'void (*)(H5::H5Object&, std::string, void*)'
      to 'void (*)(H5::H5Location&, std::string, void*)'
    EOS
  end

  def install
    hdf5 = Formula["hdf5"]
    system "make", "STATIC=",
      "HDF5INCLUDEDIR=#{hdf5.opt_include}",
      "HDF5LIBDIR=#{hdf5.opt_lib}"
    system 'make', 'install', 'PREFIX=' + prefix
  end

  test do
    system 'blasr'
  end
end<commit_msg>blasr 2.1: Add desc and tag "bioinformatics"<commit_after>class Blasr < Formula
  desc "PacBio long read aligner"
  homepage "https://github.com/PacificBiosciences/blasr"
  # doi "10.1186/1471-2105-13-238"
  # tag "bioinformatics"

  url "https://github.com/PacificBiosciences/blasr/archive/smrtanalysis-2.1.tar.gz"
  sha256 "12b20c05fcfdd166d654971402ba872dc23cb948e46e5cd40a432fb6c1b814f1"

  head "https://github.com/PacificBiosciences/blasr.git"

  depends_on "hdf5"

  fails_with :clang do
    build 602
    cause <<-EOS.undent
      error: destructor type 'HDFWriteBuffer<int>' in object
      destruction expression does not match the type
      'BufferedHDFArray<int>' of the object being destroyed
    EOS
  end

  fails_with :gcc do
    build 5666
    cause <<-EOS.undent
      error: invalid conversion
      from 'void (*)(H5::H5Object&, std::string, void*)'
      to 'void (*)(H5::H5Location&, std::string, void*)'
    EOS
  end

  def install
    hdf5 = Formula["hdf5"]
    system "make", "STATIC=",
      "HDF5INCLUDEDIR=#{hdf5.opt_include}",
      "HDF5LIBDIR=#{hdf5.opt_lib}"
    system "make", "install", "PREFIX=#{prefix}"
  end

  test do
    system "#{bin}/blasr"
  end
end
{'fraction_non_alphanumeric': 0.12669881630863655, 'fraction_numerical': 0.06313020604997809, 'mean_word_length': 3.4833005893909625, 'pattern_counts': {'":': 0, '<': 17, '<?xml version=': 0, '>': 7, 'https://': 6, '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': '5459584', 'n_tokens_mistral': 959, 'n_tokens_neox': 864, 'n_words': 185}