Feature/app

.clang-format

@@ -118,12 +118,18 @@ IncludeCategories:
     Priority:        1
   - Regex:           '(<[[:alnum:]._]+>)'
     Priority:        2
-  - Regex:           '<sharg/'
+  - Regex:           '<fmt/'
     Priority:        3
-  - Regex:           '<seqan3/'
+  - Regex:           '<sharg/'
     Priority:        4
-  - Regex:           '.*'
+  - Regex:           '<seqan3/'
     Priority:        5
+  - Regex:           '<hibf/'
+    Priority:        6
+  - Regex:           '<fmindex-collection/'
+    Priority:        7
+  - Regex:           '.*'
+    Priority:        8
 IncludeIsMainRegex: '(Test)?$'
 IncludeIsMainSourceRegex: ''
 IndentAccessModifiers: false
@@ -240,4 +246,6 @@ TabWidth:        4
 UseTab:          Never
 VerilogBreakBetweenInstancePorts: true
 WhitespaceSensitiveMacros:
+  - SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_START
+  - SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_STOP
 ...

.github/workflows/ci_linux.yml

@@ -29,10 +29,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["clang-latest", "clang-second-latest", "clang-third-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest", "intel"]
+        compiler: ["clang-latest", "clang-second-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest", "intel"]
         include:
           - compiler: "intel"
             cxx_flags: "-fp-model=strict -Wno-overriding-option"
+          - compiler: "gcc-latest"
+            cxx_flags: "-Wno-stringop-overflow"
+          - compiler: "gcc-second-latest"
+            cxx_flags: "-Wno-stringop-overflow"
     container:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:

.github/workflows/ci_macos.yml

@@ -29,7 +29,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["clang-latest", "clang-second-latest", "clang-third-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest"]
+        compiler: ["clang-latest", "clang-second-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest"]
     steps:
       - name: Checkout
         uses: actions/checkout@v4

CMakeLists.txt

@@ -1,6 +1,6 @@
 # SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
 # SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
-# SPDX-License-Identifier: CC0-1.0
+# SPDX-License-Identifier: BSD-3-Clause
 
 cmake_minimum_required (VERSION 3.25)
 
@@ -31,9 +31,11 @@ CPMGetPackage (use_ccache) # Speeds up compilation by caching files that have be
 # Comment/Uncomment entries as needed.
 # If you change something here, make sure to add/remove the target in target_link_libraries of src/CMakeLists.txt.
 CPMGetPackage (fmindex) # FM-Index
+CPMGetPackage (fmt) # Formatting
 CPMGetPackage (hibf) # (Hierarchical) Interleaved Bloom Filter
 CPMGetPackage (seqan3) # Sequence analysis
 CPMGetPackage (sharg) # Argument parser
+CPMGetPackage (thresholding) # Thresholding (requires seqan3 to be present)
 
 # Add the application. This will include `src/CMakeLists.txt`.
 add_subdirectory (src)

LICENSE.md

@@ -1,7 +1,9 @@
-In our project, we have adopted the use of SPDX identifiers to specify the license under which each file is provided.
+In FPGAlign, we have adopted the use of SPDX identifiers to specify the license under which each file is provided.
 
 This approach simplifies the process of license declaration as it replaces the full license text with a single line
 identifier. The SPDX identifier is a globally recognized standard that allows for easy identification and understanding
 of the license. This means that each file in our project will have a license identifier at the top, making it clear
 under which license the file is provided. For more information about the specific licenses, you can refer to the
 [SPDX License List](https://spdx.org/licenses/).
+
+For the purpose of referring to a singular license, FPGAlign is licensed under BSD-3-Clause.

LICENSES/BSD-3-Clause.txt

@@ -0,0 +1,11 @@
+Copyright (c) <year> <owner>. 
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

cmake/cxx_config.cmake

@@ -1,6 +1,6 @@
 # SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
 # SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
-# SPDX-License-Identifier: CC0-1.0
+# SPDX-License-Identifier: BSD-3-Clause
 
 if (NOT DEFINED CMAKE_CXX_STANDARD)
     set (CMAKE_CXX_STANDARD 23)

cmake/output_directories.cmake

@@ -1,6 +1,6 @@
 # SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
 # SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
-# SPDX-License-Identifier: CC0-1.0
+# SPDX-License-Identifier: BSD-3-Clause
 
 set (CMAKE_ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
 set (CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")

cmake/package-lock.cmake

@@ -1,14 +1,14 @@
 # SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
 # SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
-# SPDX-License-Identifier: CC0-1.0
+# SPDX-License-Identifier: BSD-3-Clause
 
 # CPM Package Lock (https://github.com/cpm-cmake/CPM.cmake)
 # This file should be committed to version control
 
 # cmake-format: off
 
 # hibf
-set (HIBF_VERSION 36c223527d7d4eb2bcdcd88d47c71984f50a00a3 CACHE STRING "" FORCE)
+set (HIBF_VERSION 36c223527d7d4eb2bcdcd88d47c71984f50a00a3 CACHE STRING "")
 CPMDeclarePackage (hibf
                    NAME hibf
                    GIT_TAG ${HIBF_VERSION} # main
@@ -19,7 +19,7 @@ CPMDeclarePackage (hibf
 )
 
 # sharg
-set (SHARG_VERSION be113bcffe49c0d62cbd65a191820f05386aa8da CACHE STRING "" FORCE)
+set (SHARG_VERSION be113bcffe49c0d62cbd65a191820f05386aa8da CACHE STRING "")
 CPMDeclarePackage (sharg
                    NAME sharg
                    GIT_TAG ${SHARG_VERSION} # main
@@ -30,7 +30,7 @@ CPMDeclarePackage (sharg
 )
 
 # seqan3
-set (SEQAN3_VERSION 6dfa1b442d1fabd07024edcc37a29b61d5beae8f CACHE STRING "" FORCE)
+set (SEQAN3_VERSION 6dfa1b442d1fabd07024edcc37a29b61d5beae8f CACHE STRING "")
 CPMDeclarePackage (seqan3
                    NAME seqan3
                    GIT_TAG ${SEQAN3_VERSION} # main
@@ -40,8 +40,20 @@ CPMDeclarePackage (seqan3
                    OPTIONS "INSTALL_SEQAN3 OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
 
+# fmt
+set (FMT_VERSION 11.2.0 CACHE STRING "")
+CPMDeclarePackage (fmt
+                   NAME fmt
+                   VERSION ${FMT_VERSION}
+                   GIT_TAG ${FMT_VERSION}
+                   GITHUB_REPOSITORY fmtlib/fmt
+                   SYSTEM TRUE
+                   EXCLUDE_FROM_ALL TRUE
+                   OPTIONS "CMAKE_MESSAGE_LOG_LEVEL WARNING" "FMT_INSTALL OFF"
+)
+
 # fmindex
-set (FMINDEX_VERSION 7ed8c3a6035a898f3e9574c5aa96af8b74ca6ef4 CACHE STRING "" FORCE)
+set (FMINDEX_VERSION 7ed8c3a6035a898f3e9574c5aa96af8b74ca6ef4 CACHE STRING "")
 CPMDeclarePackage (fmindex
                    NAME fmindex
                    GIT_TAG ${FMINDEX_VERSION} # main
@@ -52,7 +64,7 @@ CPMDeclarePackage (fmindex
 )
 
 # googletest
-set (GOOGLETEST_VERSION 1.17.0 CACHE STRING "" FORCE)
+set (GOOGLETEST_VERSION 1.17.0 CACHE STRING "")
 CPMDeclarePackage (googletest
                    NAME GTest
                    VERSION ${GOOGLETEST_VERSION}
@@ -63,7 +75,7 @@ CPMDeclarePackage (googletest
 )
 
 # use_ccache
-set (USE_CCACHE_VERSION d2a54ef555b6fc2d496a4c9506dbeb7cf899ce37 CACHE STRING "" FORCE)
+set (USE_CCACHE_VERSION d2a54ef555b6fc2d496a4c9506dbeb7cf899ce37 CACHE STRING "")
 CPMDeclarePackage (use_ccache
                    NAME use_ccache
                    GIT_TAG ${USE_CCACHE_VERSION} # main
@@ -73,4 +85,13 @@ CPMDeclarePackage (use_ccache
                    EXCLUDE_FROM_ALL TRUE
 )
 
+# thresholding
+CPMDeclarePackage (thresholding
+                   NAME thresholding
+                   URL "${PROJECT_SOURCE_DIR}/contrib/threshold.tar.gz"
+                   URL_HASH SHA256=4990c7fb9778a2fb8a19794b966d57496ca77bcd708b4cee3c93eea6e5b67d80
+                   SYSTEM TRUE
+                   EXCLUDE_FROM_ALL TRUE
+)
+
 # cmake-format: on

cmake/test/add_local_data.cmake

@@ -1,6 +1,6 @@
 # SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
 # SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
-# SPDX-License-Identifier: CC0-1.0
+# SPDX-License-Identifier: BSD-3-Clause
 
 set (DATASOURCES_DATA_DIR "${FPGAlign_SOURCE_DIR}/test/data")
 
@@ -22,7 +22,7 @@ foreach (datasource IN LISTS datasources)
     # If a matching file contains `@data_dir@`, it will be replaced with the actual data directory.
     # This is useful if you have test files that need to reference the data directory, e.g., a file containing
     # paths to other files.
-    if (FALSE)
+    if (datasource_name MATCHES ".*\.txt$")
         configure_file ("${DATASOURCES_DATA_DIR}/${datasource}" "${data_dir}/${datasource_name}")
     else ()
         configure_file ("${DATASOURCES_DATA_DIR}/${datasource}" "${data_dir}/${datasource_name}" COPYONLY)

cmake/test/config.cmake

@@ -1,6 +1,6 @@
 # SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
 # SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
-# SPDX-License-Identifier: CC0-1.0
+# SPDX-License-Identifier: BSD-3-Clause
 
 list (APPEND CMAKE_CTEST_ARGUMENTS "--output-on-failure") # Must be before `enable_testing ()`.
 list (APPEND CMAKE_CTEST_ARGUMENTS "--no-tests=error") # Must be before `enable_testing ()`.

cmake/test/declare_datasource.cmake

@@ -1,6 +1,6 @@
 # SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
 # SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
-# SPDX-License-Identifier: CC0-1.0
+# SPDX-License-Identifier: BSD-3-Clause
 
 if (CMAKE_VERSION VERSION_LESS 3.30)
     include (ExternalProject)

contrib/threshold.tar.gz.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+SPDX-License-Identifier: BSD-3-Clause

include/fpgalign/argument_parsing.hpp

@@ -0,0 +1,24 @@
+// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+// SPDX-License-Identifier: BSD-3-Clause
+
+#pragma once
+
+#include <string>
+#include <vector>
+
+#include <fpgalign/config.hpp>
+
+enum class subcommand : uint8_t
+{
+    build,
+    search
+};
+
+struct parse_result
+{
+    subcommand subcmd;
+    config cfg;
+};
+
+parse_result parse_arguments(std::vector<std::string> command_line);

include/fpgalign/build/build.hpp

@@ -0,0 +1,21 @@
+// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+// SPDX-License-Identifier: BSD-3-Clause
+
+#pragma once
+
+#include <string>
+#include <vector>
+
+#include <fpgalign/config.hpp>
+
+namespace build
+{
+
+std::vector<std::vector<std::string>> parse_input(config const & config);
+
+void build(config const & config);
+void ibf(config const & config);
+void fmindex(config const & config);
+
+} // namespace build

include/fpgalign/colored_strings.hpp

@@ -0,0 +1,18 @@
+// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+// SPDX-License-Identifier: BSD-3-Clause
+
+#pragma once
+
+#include <string>
+
+struct colored_strings
+{
+    static bool const cerr_is_terminal;
+
+    struct cerr
+    {
+        static std::string const error;
+        static std::string const warning;
+    };
+};

include/fpgalign/config.hpp

@@ -0,0 +1,22 @@
+// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+// SPDX-License-Identifier: BSD-3-Clause
+
+#pragma once
+
+#include <filesystem>
+
+struct config
+{
+    uint8_t kmer_size{20u};
+    uint32_t window_size{kmer_size};
+
+    uint8_t hash_count{2u};
+    double fpr{0.05};
+
+    std::filesystem::path input_path{};
+    std::filesystem::path output_path{};
+    std::filesystem::path query_path{};
+    uint8_t errors{};
+    uint16_t threads{1u};
+};