From 61907ec0efe00f6e3d4dc630b618e584c4a99289 Mon Sep 17 00:00:00 2001
From: smehringer <svenja.mehringer@gmail.com>
Date: Tue, 20 Aug 2024 12:17:52 +0200
Subject: [PATCH] delte read_hll file test.

---
 test/api/sketch/read_hll_files_into_test.cpp | 118 -------------------
 1 file changed, 118 deletions(-)
 delete mode 100644 test/api/sketch/read_hll_files_into_test.cpp

diff --git a/test/api/sketch/read_hll_files_into_test.cpp b/test/api/sketch/read_hll_files_into_test.cpp
deleted file mode 100644
index 74c73601..00000000
--- a/test/api/sketch/read_hll_files_into_test.cpp
+++ /dev/null
@@ -1,118 +0,0 @@
-// ---------------------------------------------------------------------------------------------------
-// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
-// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
-// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
-// shipped with this file and also available at: https://github.com/seqan/chopper/blob/main/LICENSE.md
-// ---------------------------------------------------------------------------------------------------
-
-#include <gtest/gtest.h>
-
-#include <cstddef>
-#include <filesystem>
-#include <fstream>
-#include <ranges>
-#include <stdexcept>
-#include <string>
-#include <vector>
-
-#include <seqan3/io/sequence_file/input.hpp>
-#include <seqan3/search/views/minimiser_hash.hpp>
-
-#include <chopper/adjust_seed.hpp>
-#include <chopper/sketch/read_hll_files_into.hpp>
-
-#include "../api_test.hpp"
-
-struct input_traits : public seqan3::sequence_file_input_default_traits_dna
-{
-    using sequence_alphabet = seqan3::dna4;
-};
-using sequence_file_type = seqan3::sequence_file_input<input_traits, seqan3::fields<seqan3::field::seq>>;
-
-// inherits from toolbox to test private members
-struct read_hll_files_into_test : public ::testing::Test
-{
-    std::vector<std::string> test_filenames{"small.fa", "small.fa", "small2.fa", "small2.fa"};
-    std::vector<size_t> test_kmer_counts{500, 600, 700, 800};
-    std::vector<size_t> test_positions{0, 1, 2, 3};
-    std::vector<seqan::hibf::sketch::hyperloglog> test_sketches = [this]()
-    {
-        std::vector<seqan::hibf::sketch::hyperloglog> result;
-        chopper::sketch::read_hll_files_into(data(""), test_filenames, result);
-        return result;
-    }();
-};
-
-TEST_F(read_hll_files_into_test, basic)
-{
-    size_t const kmer_size{16};
-    size_t const b{5};
-    seqan::hibf::sketch::hyperloglog expected{b};
-
-    std::vector<seqan::hibf::sketch::hyperloglog> target{};
-
-    std::string const input_file{data("small.fa")};
-    sequence_file_type seq_file{input_file};
-
-    auto minimizer_view = seqan3::views::minimiser_hash(seqan3::ungapped{kmer_size},
-                                                        seqan3::window_size{kmer_size},
-                                                        seqan3::seed{chopper::adjust_seed(kmer_size)});
-
-    // put every sequence in this file into the sketch
-    for (auto && [seq] : seq_file)
-    {
-        for (auto hash : seq | minimizer_view)
-            expected.add(hash);
-    }
-
-    chopper::sketch::read_hll_files_into(data(""), test_filenames, target);
-
-    EXPECT_EQ(target.size(), 4u);
-    for (auto const & sketch : target)
-        EXPECT_EQ(sketch.estimate(), expected.estimate());
-}
-
-TEST_F(read_hll_files_into_test, empty_dir)
-{
-    seqan3::test::tmp_directory empty_dir{};
-    ASSERT_TRUE(std::filesystem::exists(empty_dir.path()));
-    ASSERT_TRUE(std::filesystem::is_empty(empty_dir.path()));
-
-    std::vector<seqan::hibf::sketch::hyperloglog> target{};
-    // Will throw in Release, but assert in Debug
-#ifdef NDEBUG
-    EXPECT_THROW(chopper::sketch::read_hll_files_into(empty_dir.path(), test_filenames, target), std::runtime_error);
-#else
-    EXPECT_DEATH(chopper::sketch::read_hll_files_into(empty_dir.path(), test_filenames, target), "");
-#endif
-}
-
-TEST_F(read_hll_files_into_test, file_is_missing)
-{
-    seqan3::test::tmp_directory tmp_dir{};
-    std::filesystem::path const tmp_file{tmp_dir.path() / "other.hll"};
-    {
-        std::ofstream os{tmp_file};
-        os << "Doesn't matter I just need to exist\n";
-    }
-
-    std::vector<seqan::hibf::sketch::hyperloglog> target{};
-
-    EXPECT_THROW(chopper::sketch::read_hll_files_into(tmp_file.parent_path(), test_filenames, target),
-                 std::runtime_error);
-}
-
-TEST_F(read_hll_files_into_test, read_hll_files_into_faulty_file)
-{
-    seqan3::test::tmp_directory tmp_dir{};
-    std::filesystem::path const tmp_file{tmp_dir.path() / "small.hll"};
-    {
-        std::ofstream os{tmp_file};
-        os << "I am not what an hll file looks like\n";
-    }
-
-    std::vector<seqan::hibf::sketch::hyperloglog> target{};
-
-    EXPECT_THROW(chopper::sketch::read_hll_files_into(tmp_file.parent_path(), test_filenames, target),
-                 std::runtime_error);
-}