[MISC] Read input functions

include/chopper/layout/input.hpp

@@ -0,0 +1,90 @@
+// ---------------------------------------------------------------------------------------------------
+// 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
+// ---------------------------------------------------------------------------------------------------
+
+#pragma once
+
+#include <cassert>
+#include <charconv>
+#include <ranges>
+
+#include <cereal/archives/json.hpp>
+
+#include <chopper/configuration.hpp>
+
+#include <hibf/detail/prefixes.hpp>
+
+namespace chopper::layout
+{
+
+inline void read_config_from(configuration & config, std::istream & stream)
+{
+    std::string line;
+    std::stringstream config_str;
+
+    while (std::getline(stream, line) && line != "@CHOPPER_CONFIG")
+        ;
+
+    assert(line == "@CHOPPER_CONFIG");
+
+    // TODO ##CONFIG: as prefix
+    while (std::getline(stream, line) && line != "@CHOPPER_CONFIG_END")
+    {
+        assert(line.size() >= 2);
+        assert(std::string_view{line}.substr(0, 1) == seqan::hibf::prefix::meta_header);
+        config_str << line.substr(1); // remove seqan::hibf::prefix::meta_header
+    }
+
+    assert(line == "@CHOPPER_CONFIG_END");
+
+    cereal::JSONInputArchive iarchive(config_str);
+    iarchive(config);
+}
+
+inline std::vector<std::vector<std::string>> read_filenames_from(std::istream & stream)
+{
+    std::vector<std::vector<std::string>> filenames{};
+    std::string line;
+
+    while (std::getline(stream, line) && line != "@CHOPPER_USER_BINS")
+        ;
+
+    assert(line == "@CHOPPER_USER_BINS");
+
+#ifndef NDEBUG
+    size_t counter{};
+#endif
+    // TODO ##CONFIG: as prefix
+    while (std::getline(stream, line) && line != "@CHOPPER_USER_BINS_END")
+    {
+        assert(line.size() >= 2);
+        assert(std::string_view{line}.substr(0, 1) == seqan::hibf::prefix::meta_header);
+
+        // @0 file1.fa file2.fa
+        auto const bin_idx_pos = line.find(' ');
+        assert(bin_idx_pos != std::string::npos);
+
+#ifndef NDEBUG
+        size_t bin_idx{};
+        std::from_chars(line.data() + 1, line.data() + bin_idx_pos, bin_idx);
+        assert(bin_idx == counter++);
+#endif
+
+        filenames.emplace_back();
+        std::string_view const filename_str{line.begin() + bin_idx_pos + 1, line.end()};
+        for (auto const && filename : std::views::split(filename_str, ' '))
+        {
+            auto common_view = std::views::common(filename);
+            filenames.back().emplace_back(common_view.begin(), common_view.end());
+        }
+    }
+
+    assert(line == "@CHOPPER_USER_BINS_END");
+
+    return filenames;
+}
+
+} // namespace chopper::layout

src/display_layout.cpp

@@ -18,7 +18,7 @@
 #include <seqan3/search/views/kmer_hash.hpp>
 
 #include <chopper/layout/hibf_statistics.hpp>
-#include <chopper/stats/read_layout_file.hpp> // for read_layout_file
+#include <chopper/layout/input.hpp>
 
 #include <hibf/detail/sketch/hyperloglog.hpp>
 
@@ -119,11 +119,19 @@ void process_file(std::string const & filename,
     }
 }
 
-int execute(std::filesystem::path const & layout_file)
+int execute(std::filesystem::path const & layout_filename)
 {
-    std::vector<std::vector<std::string>> filenames;
     chopper::configuration chopper_config;
-    seqan::hibf::layout::layout hibf_layout = chopper::stats::read_layout_file(chopper_config, filenames, layout_file);
+    std::ifstream layout_file{layout_filename};
+
+    if (!layout_file.good() || !layout_file.is_open())
+        throw std::logic_error{"Could not open file " + layout_filename.string() + " for reading"}; // GCOVR_EXCL_LINE
+
+    std::vector<std::vector<std::string>> filenames = chopper::layout::read_filenames_from(layout_file);
+    chopper::layout::read_config_from(chopper_config, layout_file);
+    chopper_config.hibf_config.read_from(layout_file);
+    seqan::hibf::layout::layout hibf_layout{};
+    hibf_layout.read_from(layout_file);
     auto const & hibf_config = chopper_config.hibf_config;
 
     // Fetch all file sizes such that sorting by file size doesn't have to access the filesystem too often.
@@ -183,7 +191,7 @@ int execute(std::filesystem::path const & layout_file)
     size_t current_idx{}; // The current top-level technical bin index
 
     // Stats file header
-    std::cout << "# Layout: " << layout_file.c_str() << '\n' //
+    std::cout << "# Layout: " << layout_filename.c_str() << '\n' //
               << "tb_index\t"
               << "size\t"
               << "shared_size\t"