<commit_before>class Amos < Formula
  homepage "http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS"
  #doi "10.1002/0471250953.bi1108s33"
  #tag "bioinformatics"

  url "https://downloads.sourceforge.net/project/amos/amos/3.1.0/amos-3.1.0.tar.gz"
  sha1 "28e799e37713594ba7147d300ecae6574beb14a4"

  depends_on "blat" => :optional # for minimus2-blat
  depends_on "boost" => :recommended # for Bambus 2
  depends_on "mummer" => :recommended # for minimus2
  depends_on "qt" => [:optional, "with-qt3support"] # for AMOS GUIs
  depends_on "Statistics::Descriptive" => :perl

  fails_with :clang do
    build 600
    cause "error: reference to 'hash' is ambiguous"
  end

  def install
    # http://seqanswers.com/forums/showthread.php?t=17802
    inreplace "src/Align/find-tandem.cc", "#include <sys/time.h>", "#include <sys/time.h>\n#include <getopt.h>"

    ENV.deparallelize
    args = %W[--prefix=#{prefix} --disable-dependency-tracking]
    args << "--with-Boost-dir=#{Formula["boost"].opt_prefix}" if build.with? "boost"<commit_msg>amos: add desc<commit_after>class Amos < Formula
  desc "A Modular Open-Source Assembler"
  homepage "http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS"
  # doi "10.1002/0471250953.bi1108s33"
  # tag "bioinformatics"

  url "https://downloads.sourceforge.net/project/amos/amos/3.1.0/amos-3.1.0.tar.gz"
  sha1 "28e799e37713594ba7147d300ecae6574beb14a4"

  depends_on "blat" => :optional # for minimus2-blat
  depends_on "boost" => :recommended # for Bambus 2
  depends_on "mummer" => :recommended # for minimus2
  depends_on "qt" => [:optional, "with-qt3support"] # for AMOS GUIs
  depends_on "Statistics::Descriptive" => :perl

  fails_with :clang do
    build 600
    cause "error: reference to 'hash' is ambiguous"
  end

  def install
    # http://seqanswers.com/forums/showthread.php?t=17802
    inreplace "src/Align/find-tandem.cc", "#include <sys/time.h>", "#include <sys/time.h>\n#include <getopt.h>"

    ENV.deparallelize
    args = %W[--prefix=#{prefix} --disable-dependency-tracking]
    args << "--with-Boost-dir=#{Formula["boost"].opt_prefix}" if build.with? "boost"
{'fraction_non_alphanumeric': 0.1549953314659197, 'fraction_numerical': 0.06349206349206349, 'mean_word_length': 4.188861985472155, 'pattern_counts': {'":': 0, '<': 15, '<?xml version=': 0, '>': 19, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, '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': '3530517', 'n_tokens_mistral': 906, 'n_tokens_neox': 809, 'n_words': 148}