From 7ecbe01a372749fb872df56c80c5e7450376b9cd Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Mon, 18 Mar 2024 10:59:55 +0100 Subject: [PATCH] [DOC] SPDX Licenses --- .clang-format | 4 + .cmake-format.yaml | 4 + .codecov.yml | 4 + .gitattributes | 4 + .github/ISSUE_TEMPLATE/bug_report.md | 6 + .github/ISSUE_TEMPLATE/feature_request.md | 6 + .github/dependabot.yml | 4 + .github/workflows/ci_codeql.yml | 4 + .github/workflows/ci_coverage.yml | 4 + .github/workflows/ci_documentation.yml | 4 + .github/workflows/ci_fortify.yml | 4 + .github/workflows/ci_license.yml | 34 ++++ .github/workflows/ci_lint.yml | 4 + .github/workflows/ci_linux.yml | 4 + .github/workflows/ci_macos.yml | 4 + .github/workflows/ci_misc.yml | 4 + .github/workflows/ci_sanitizer.yml | 4 + .github/workflows/ci_utility.yml | 4 + .github/workflows/ci_workflows.yml | 4 + .github/workflows/scripts/gcov.sh | 4 +- .gitignore | 4 + .reuse/dep5 | 11 ++ CHANGELOG.md | 6 + CMakeLists.txt | 9 +- CODE_OF_CONDUCT.md | 6 + 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--diff-filter=ACMRT | grep -E "(\.cpp|\.hpp)$" | xargs clang-format-15 --style=file -i diff --git a/.cmake-format.yaml b/.cmake-format.yaml index 15c1d6bf..96038c57 100644 --- a/.cmake-format.yaml +++ b/.cmake-format.yaml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024, Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + # find . \( -iname CMakeLists.txt -o -iname *.cmake \) -a -not -path "./lib/*" -a -not -path "./build/*" | xargs cmake-format -c .cmake-format.yaml -i _help_parse: Options affecting listfile parsing parse: diff --git a/.codecov.yml b/.codecov.yml index 375f21a7..704156a9 100644 --- a/.codecov.yml +++ b/.codecov.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024, Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + # See https://docs.codecov.io/docs/codecovyml-reference codecov: token: 493cd34e-2543-4e61-b7a8-da2c0bc62fb9 diff --git a/.gitattributes b/.gitattributes index 8929aa5d..c3869105 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + doc/** linguist-documentation test/util/** linguist-documentation test/benchmark/parse.py linguist-documentation diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md index 1f96e15c..4c3953c9 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -1,3 +1,9 @@ + + --- name: Bug report about: Create a report to help us improve Raptor diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md index ab12d623..c3b73777 100644 --- a/.github/ISSUE_TEMPLATE/feature_request.md +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -1,3 +1,9 @@ + + --- name: Feature request about: Request a new feature that you would like to see in Raptor diff --git a/.github/dependabot.yml b/.github/dependabot.yml index dcbcb650..ba5cc583 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + # https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates version: 2 diff --git a/.github/workflows/ci_codeql.yml b/.github/workflows/ci_codeql.yml index 63fbff51..a5896de5 100644 --- a/.github/workflows/ci_codeql.yml +++ b/.github/workflows/ci_codeql.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + name: CodeQL on: diff --git a/.github/workflows/ci_coverage.yml b/.github/workflows/ci_coverage.yml index 26af0da3..8fa984a1 100644 --- a/.github/workflows/ci_coverage.yml +++ b/.github/workflows/ci_coverage.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + name: Coverage on: diff --git a/.github/workflows/ci_documentation.yml b/.github/workflows/ci_documentation.yml index 53398cd4..fcd4e725 100644 --- a/.github/workflows/ci_documentation.yml +++ b/.github/workflows/ci_documentation.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + name: Documentation on: diff --git a/.github/workflows/ci_fortify.yml b/.github/workflows/ci_fortify.yml index 96dbd21c..466887f8 100644 --- a/.github/workflows/ci_fortify.yml +++ b/.github/workflows/ci_fortify.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + name: Fortify on: diff --git a/.github/workflows/ci_license.yml b/.github/workflows/ci_license.yml new file mode 100644 index 00000000..2103a620 --- /dev/null +++ b/.github/workflows/ci_license.yml @@ -0,0 +1,34 @@ +# SPDX-FileCopyrightText: 2006-2024, Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + +name: License + +on: + push: + branches: + - 'main' + pull_request: + types: + - unlabeled + workflow_dispatch: + +concurrency: + group: license-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: ${{ github.event_name != 'push' }} + +env: + TZ: Europe/Berlin + +jobs: + check: + name: REUSE Compliance + runs-on: ubuntu-22.04 + timeout-minutes: 120 + if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint' + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: REUSE Compliance Check + uses: fsfe/reuse-action@v3 diff --git a/.github/workflows/ci_lint.yml b/.github/workflows/ci_lint.yml index 06ed2f45..e46b1a78 100644 --- a/.github/workflows/ci_lint.yml +++ b/.github/workflows/ci_lint.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + name: Lint on: diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml index 4042fcb1..4288577f 100644 --- a/.github/workflows/ci_linux.yml +++ b/.github/workflows/ci_linux.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + name: Linux on: diff --git a/.github/workflows/ci_macos.yml b/.github/workflows/ci_macos.yml index dbf474c0..453cb8a6 100644 --- a/.github/workflows/ci_macos.yml +++ b/.github/workflows/ci_macos.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + name: macOS on: diff --git a/.github/workflows/ci_misc.yml b/.github/workflows/ci_misc.yml index b9336506..7aac17f1 100644 --- a/.github/workflows/ci_misc.yml +++ b/.github/workflows/ci_misc.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + name: Misc on: diff --git a/.github/workflows/ci_sanitizer.yml b/.github/workflows/ci_sanitizer.yml index a0dd5941..f7c09d31 100644 --- a/.github/workflows/ci_sanitizer.yml +++ b/.github/workflows/ci_sanitizer.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + name: Sanitizer on: diff --git a/.github/workflows/ci_utility.yml b/.github/workflows/ci_utility.yml index 17ec2b3b..6dcbaa4f 100644 --- a/.github/workflows/ci_utility.yml +++ b/.github/workflows/ci_utility.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + name: Utility on: diff --git a/.github/workflows/ci_workflows.yml b/.github/workflows/ci_workflows.yml index be19f8a8..63556a2a 100644 --- a/.github/workflows/ci_workflows.yml +++ b/.github/workflows/ci_workflows.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + name: Workflows on: diff --git a/.github/workflows/scripts/gcov.sh b/.github/workflows/scripts/gcov.sh index 258340d0..6883a89d 100755 --- a/.github/workflows/scripts/gcov.sh +++ b/.github/workflows/scripts/gcov.sh @@ -1,7 +1,7 @@ #!/usr/bin/env bash -# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin -# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik # SPDX-License-Identifier: CC0-1.0 set -Eeuo pipefail diff --git a/.gitignore b/.gitignore index 3c6322b7..4a2846eb 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + # Prerequisites *.d diff --git a/.reuse/dep5 b/.reuse/dep5 new file mode 100644 index 00000000..92321319 --- /dev/null +++ b/.reuse/dep5 @@ -0,0 +1,11 @@ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: Raptor +Upstream-Contact: Enrico Seiler +Source: https://github.com/seqan/raptor/ + +Files: test/data/* + workflow/galaxy/test-data/* + workflow/nextflow/data/* +Copyright: 2006-2024, Knut Reinert & Freie Universität Berlin + 2016-2024, Knut Reinert & MPI für molekulare Genetik +License: CC0-1.0 diff --git a/CHANGELOG.md b/CHANGELOG.md index a6163d74..6fe79b8b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ + + # 2.0.0 ## Features diff --git a/CMakeLists.txt b/CMakeLists.txt index 64984b3d..70982cca 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index f4f60599..b590672e 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -1,3 +1,9 @@ + + # Code of Conduct The SeqAn project adheres to the [Berlin Code of Conduct](https://berlincodeofconduct.org/). From the code of conduct: diff --git a/INSTALL.md b/INSTALL.md deleted file mode 100644 index e69de29b..00000000 diff --git a/LICENSE.md b/LICENSE.md index 70eb996f..06e7ae88 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,30 +1,9 @@ -BSD 3-Clause License +In Raptor, we have adopted the use of SPDX identifiers to specify the license under which each file is provided. -Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -All rights reserved. +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/). -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. +For the purpose of referring to a singular license, Raptor is licensed under BSD-3-Clause. diff --git a/LICENSES/BSD-3-Clause.txt b/LICENSES/BSD-3-Clause.txt new file mode 100644 index 00000000..ea890afb --- /dev/null +++ b/LICENSES/BSD-3-Clause.txt @@ -0,0 +1,11 @@ +Copyright (c) . + +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. 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IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/README.md b/README.md index c9f764df..eb99812d 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,9 @@ + + # Raptor [![build status][1]][2] [![codecov][3]][4] [![install with bioconda][5]][6] [1]: https://img.shields.io/github/actions/workflow/status/seqan/raptor/ci_linux.yml?branch=main&style=flat&logo=github&label=Raptor%20CI diff --git a/cmake/configuration.cmake b/cmake/configuration.cmake index 337cbe53..fbad45c1 100644 --- a/cmake/configuration.cmake +++ b/cmake/configuration.cmake @@ -1,5 +1,5 @@ -# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin -# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik # SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/cmake/package-lock.cmake b/cmake/package-lock.cmake index 96b8b97b..38634874 100644 --- a/cmake/package-lock.cmake +++ b/cmake/package-lock.cmake @@ -1,6 +1,6 @@ -# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin -# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik -# SPDX-License-Identifier: CC0-1.0 +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause # CPM Package Lock # This file should be committed to version control diff --git a/cmake/raptor-package.cmake b/cmake/raptor-package.cmake index 4cae5064..8f2212a9 100644 --- a/cmake/raptor-package.cmake +++ b/cmake/raptor-package.cmake @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause # This file describes how Sharg will be packaged. diff --git a/cmake/version.cmake b/cmake/version.cmake index a41c60db..675710f9 100644 --- a/cmake/version.cmake +++ b/cmake/version.cmake @@ -1,5 +1,5 @@ -# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin -# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik # SPDX-License-Identifier: BSD-3-Clause file (STRINGS "${CMAKE_CURRENT_LIST_DIR}/../include/raptor/version.hpp" RAPTOR_VERSION_HPP diff --git a/doc/figures/Raptor_no_title.svg.license b/doc/figures/Raptor_no_title.svg.license new file mode 100644 index 00000000..70b01de1 --- /dev/null +++ b/doc/figures/Raptor_no_title.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: CC-BY-4.0 diff --git a/doc/figures/fig_4_many_user_bins.svg.license b/doc/figures/fig_4_many_user_bins.svg.license new file mode 100644 index 00000000..70b01de1 --- /dev/null +++ b/doc/figures/fig_4_many_user_bins.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: CC-BY-4.0 diff --git a/doc/figures/fig_6_acc.svg.license b/doc/figures/fig_6_acc.svg.license new file mode 100644 index 00000000..70b01de1 --- /dev/null +++ b/doc/figures/fig_6_acc.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: CC-BY-4.0 diff --git a/doc/figures/hibf.svg.license b/doc/figures/hibf.svg.license new file mode 100644 index 00000000..70b01de1 --- /dev/null +++ b/doc/figures/hibf.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: CC-BY-4.0 diff --git a/doc/figures/ibf.svg.license b/doc/figures/ibf.svg.license new file mode 100644 index 00000000..70b01de1 --- /dev/null +++ b/doc/figures/ibf.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: CC-BY-4.0 diff --git a/doc/fragments/ibf_fpr.md b/doc/fragments/ibf_fpr.md index 08c0e6e7..78bc1f88 100644 --- a/doc/fragments/ibf_fpr.md +++ b/doc/fragments/ibf_fpr.md @@ -1,3 +1,9 @@ + + Sets an upper bound for Bloom Filter false positives.
**Recommendation**: default value (`0.05`)
  • A lower `fpr` limits the number of false-positive results, but increases index size.
diff --git a/doc/fragments/ibf_h.md b/doc/fragments/ibf_h.md index 8e863e5c..9146a23a 100644 --- a/doc/fragments/ibf_h.md +++ b/doc/fragments/ibf_h.md @@ -1,3 +1,9 @@ + + The number of hash functions to use for Bloom Filters. Influences the index size.
**Recommendation**: default value (`2`)
It should only be changed for experimentation.
diff --git a/doc/fragments/input_files_preprocessed.md b/doc/fragments/input_files_preprocessed.md index e0592f31..2a95c4d7 100644 --- a/doc/fragments/input_files_preprocessed.md +++ b/doc/fragments/input_files_preprocessed.md @@ -1,3 +1,9 @@ + + See \ref usage_prepare_output. \note diff --git a/doc/fragments/input_files_sequence.md b/doc/fragments/input_files_sequence.md index ed11c0b1..b95ff33b 100644 --- a/doc/fragments/input_files_sequence.md +++ b/doc/fragments/input_files_sequence.md @@ -1,3 +1,9 @@ + + The input file contains paths to the sequence data. Each line may contain multiple paths (separated by a whitespace). ``` diff --git a/doc/index.md b/doc/index.md index 19c67239..1c89c405 100644 --- a/doc/index.md +++ b/doc/index.md @@ -1,3 +1,9 @@ + + \mainpage Raptor \htmlonly diff --git a/doc/methods/01_introduction/index.md b/doc/methods/01_introduction/index.md index a700e6d1..7ca9c4fd 100644 --- a/doc/methods/01_introduction/index.md +++ b/doc/methods/01_introduction/index.md @@ -1,3 +1,9 @@ + + # First steps with Raptor {#tutorial_first_steps} ***Learning Objective:*** diff --git a/doc/methods/02_layout/index.md b/doc/methods/02_layout/index.md index 5ba1f032..049053da 100644 --- a/doc/methods/02_layout/index.md +++ b/doc/methods/02_layout/index.md @@ -1,3 +1,9 @@ + + # Create a layout with Raptor {#tutorial_layout} You will learn how to construct a Raptor layout of large collections of nucleotide sequences. diff --git a/doc/methods/03_index/index.md b/doc/methods/03_index/index.md index 1b43d3b6..2dedc6c8 100644 --- a/doc/methods/03_index/index.md +++ b/doc/methods/03_index/index.md @@ -1,3 +1,9 @@ + + # Indexing with Raptor {#tutorial_index} You will learn how to construct a Raptor index of large collections of nucleotide sequences. diff --git a/doc/methods/04_search/index.md b/doc/methods/04_search/index.md index 39648f9a..f4e9d7d5 100644 --- a/doc/methods/04_search/index.md +++ b/doc/methods/04_search/index.md @@ -1,3 +1,9 @@ + + # Search with Raptor {#tutorial_search} You will learn how to search a Raptor index using one or more sequences queries. diff --git a/doc/methods/script.sh b/doc/methods/script.sh index 5f4271aa..e55383b5 100755 --- a/doc/methods/script.sh +++ b/doc/methods/script.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC-BY-4.0 + set -Exeuo pipefail if [[ ! -f "example_data.tar.gz" ]]; then diff --git a/doc/methods/search_output.txt.license b/doc/methods/search_output.txt.license new file mode 100644 index 00000000..70b01de1 --- /dev/null +++ b/doc/methods/search_output.txt.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: CC-BY-4.0 diff --git a/doc/setup/index.md b/doc/setup/index.md index a3a6c91f..bb347e08 100644 --- a/doc/setup/index.md +++ b/doc/setup/index.md @@ -1,3 +1,9 @@ + + # Setup {#setup} [TOC] diff --git a/doc/usage/01_quickstart/index.md b/doc/usage/01_quickstart/index.md index 2da13e4d..bd3227bb 100644 --- a/doc/usage/01_quickstart/index.md +++ b/doc/usage/01_quickstart/index.md @@ -1,3 +1,9 @@ + + # Quickstart {#usage_quickstart} [TOC] diff --git a/doc/usage/02_prepare/index.md b/doc/usage/02_prepare/index.md index db923811..db85bb72 100644 --- a/doc/usage/02_prepare/index.md +++ b/doc/usage/02_prepare/index.md @@ -1,3 +1,9 @@ + + # raptor prepare {#usage_prepare} [TOC] diff --git a/doc/usage/03_layout/index.md b/doc/usage/03_layout/index.md index b04eca24..48a876ec 100644 --- a/doc/usage/03_layout/index.md +++ b/doc/usage/03_layout/index.md @@ -1,3 +1,9 @@ + + # raptor layout {#usage_layout} [TOC] diff --git a/doc/usage/04_build/index.md b/doc/usage/04_build/index.md index 4d138917..8fe8b950 100644 --- a/doc/usage/04_build/index.md +++ b/doc/usage/04_build/index.md @@ -1,3 +1,9 @@ + + # raptor build {#usage_build} [TOC] diff --git a/doc/usage/05_search/index.md b/doc/usage/05_search/index.md index 4399d2a1..f8bf3439 100644 --- a/doc/usage/05_search/index.md +++ b/doc/usage/05_search/index.md @@ -1,3 +1,9 @@ + + # raptor search {#usage_search} [TOC] diff --git a/include/raptor/adjust_seed.hpp b/include/raptor/adjust_seed.hpp index f62bc84d..f1bd845c 100644 --- a/include/raptor/adjust_seed.hpp +++ b/include/raptor/adjust_seed.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::adjust_seed. diff --git a/include/raptor/argument_parsing/build_arguments.hpp b/include/raptor/argument_parsing/build_arguments.hpp index e1e8f53a..bd738291 100644 --- a/include/raptor/argument_parsing/build_arguments.hpp +++ b/include/raptor/argument_parsing/build_arguments.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::build_arguments. diff --git a/include/raptor/argument_parsing/build_parsing.hpp b/include/raptor/argument_parsing/build_parsing.hpp index d27ebd03..36411a1e 100644 --- a/include/raptor/argument_parsing/build_parsing.hpp +++ b/include/raptor/argument_parsing/build_parsing.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::build_parsing. diff --git a/include/raptor/argument_parsing/compute_bin_size.hpp b/include/raptor/argument_parsing/compute_bin_size.hpp index 7c5c10fd..82e755a9 100644 --- a/include/raptor/argument_parsing/compute_bin_size.hpp +++ b/include/raptor/argument_parsing/compute_bin_size.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::compute_bin_size and raptor::max_bin_count. diff --git a/include/raptor/argument_parsing/cpu_time.hpp b/include/raptor/argument_parsing/cpu_time.hpp index a6b9a7c6..18917dc8 100644 --- a/include/raptor/argument_parsing/cpu_time.hpp +++ b/include/raptor/argument_parsing/cpu_time.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::get_cpu_time. diff --git a/include/raptor/argument_parsing/formatted_bytes.hpp b/include/raptor/argument_parsing/formatted_bytes.hpp index 6989042c..ae0d861f 100644 --- a/include/raptor/argument_parsing/formatted_bytes.hpp +++ b/include/raptor/argument_parsing/formatted_bytes.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::formatted_bytes. diff --git a/include/raptor/argument_parsing/formatted_index_size.hpp b/include/raptor/argument_parsing/formatted_index_size.hpp index fe885b6c..d6a1c00f 100644 --- a/include/raptor/argument_parsing/formatted_index_size.hpp +++ b/include/raptor/argument_parsing/formatted_index_size.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::formatted_index_size. diff --git a/include/raptor/argument_parsing/init_shared_meta.hpp b/include/raptor/argument_parsing/init_shared_meta.hpp index 438c390f..1dcc7db7 100644 --- a/include/raptor/argument_parsing/init_shared_meta.hpp +++ b/include/raptor/argument_parsing/init_shared_meta.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::init_shared_meta. diff --git a/include/raptor/argument_parsing/memory_usage.hpp b/include/raptor/argument_parsing/memory_usage.hpp index b9f6fb5b..e5f31efa 100644 --- a/include/raptor/argument_parsing/memory_usage.hpp +++ b/include/raptor/argument_parsing/memory_usage.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::formatted_peak_ram. diff --git a/include/raptor/argument_parsing/parse_bin_path.hpp b/include/raptor/argument_parsing/parse_bin_path.hpp index 16913614..de71c7d2 100644 --- a/include/raptor/argument_parsing/parse_bin_path.hpp +++ b/include/raptor/argument_parsing/parse_bin_path.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::parse_bin_path. diff --git a/include/raptor/argument_parsing/prepare_arguments.hpp b/include/raptor/argument_parsing/prepare_arguments.hpp index 2b355b77..4cb79ba9 100644 --- a/include/raptor/argument_parsing/prepare_arguments.hpp +++ b/include/raptor/argument_parsing/prepare_arguments.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::prepare_arguments. diff --git a/include/raptor/argument_parsing/prepare_parsing.hpp b/include/raptor/argument_parsing/prepare_parsing.hpp index abe7c0d9..baf5b76f 100644 --- a/include/raptor/argument_parsing/prepare_parsing.hpp +++ b/include/raptor/argument_parsing/prepare_parsing.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::prepare_parsing. diff --git a/include/raptor/argument_parsing/search_arguments.hpp b/include/raptor/argument_parsing/search_arguments.hpp index ef714820..0f59bc35 100644 --- a/include/raptor/argument_parsing/search_arguments.hpp +++ b/include/raptor/argument_parsing/search_arguments.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::search_arguments. diff --git a/include/raptor/argument_parsing/search_parsing.hpp b/include/raptor/argument_parsing/search_parsing.hpp index 7cb610b6..07ed8f48 100644 --- a/include/raptor/argument_parsing/search_parsing.hpp +++ b/include/raptor/argument_parsing/search_parsing.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::search_parsing. diff --git a/include/raptor/argument_parsing/shared.hpp b/include/raptor/argument_parsing/shared.hpp index e189bc27..feee0bb8 100644 --- a/include/raptor/argument_parsing/shared.hpp +++ b/include/raptor/argument_parsing/shared.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::validate_shape. diff --git a/include/raptor/argument_parsing/upgrade_arguments.hpp b/include/raptor/argument_parsing/upgrade_arguments.hpp index eda79124..1941b2a9 100644 --- a/include/raptor/argument_parsing/upgrade_arguments.hpp +++ b/include/raptor/argument_parsing/upgrade_arguments.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::upgrade_arguments. diff --git a/include/raptor/argument_parsing/upgrade_parsing.hpp b/include/raptor/argument_parsing/upgrade_parsing.hpp index fb4d38a6..33f21871 100644 --- a/include/raptor/argument_parsing/upgrade_parsing.hpp +++ b/include/raptor/argument_parsing/upgrade_parsing.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::upgrade_parsing. diff --git a/include/raptor/argument_parsing/validators.hpp b/include/raptor/argument_parsing/validators.hpp index c57bc0a5..46e9f8b9 100644 --- a/include/raptor/argument_parsing/validators.hpp +++ b/include/raptor/argument_parsing/validators.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides various validator. diff --git a/include/raptor/build/build_hibf.hpp b/include/raptor/build/build_hibf.hpp index 40fe8279..fec2908a 100644 --- a/include/raptor/build/build_hibf.hpp +++ b/include/raptor/build/build_hibf.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::build_ibf. diff --git a/include/raptor/build/build_ibf.hpp b/include/raptor/build/build_ibf.hpp index 022bb432..38339c6e 100644 --- a/include/raptor/build/build_ibf.hpp +++ b/include/raptor/build/build_ibf.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::build_ibf. diff --git a/include/raptor/build/emplace_iterator.hpp b/include/raptor/build/emplace_iterator.hpp index 1dae9235..6aa447de 100644 --- a/include/raptor/build/emplace_iterator.hpp +++ b/include/raptor/build/emplace_iterator.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::emplace_iterator. diff --git a/include/raptor/build/index_factory.hpp b/include/raptor/build/index_factory.hpp index dfcee53a..79c3ba1a 100644 --- a/include/raptor/build/index_factory.hpp +++ b/include/raptor/build/index_factory.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::index_factory. diff --git a/include/raptor/build/max_count_per_partition.hpp b/include/raptor/build/max_count_per_partition.hpp index 9dea860d..86114d7f 100644 --- a/include/raptor/build/max_count_per_partition.hpp +++ b/include/raptor/build/max_count_per_partition.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::max_count_per_partition. diff --git a/include/raptor/build/partition_config.hpp b/include/raptor/build/partition_config.hpp index f83cb25e..7293f755 100644 --- a/include/raptor/build/partition_config.hpp +++ b/include/raptor/build/partition_config.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::partition_config. diff --git a/include/raptor/build/raptor_build.hpp b/include/raptor/build/raptor_build.hpp index abba9204..4d855959 100644 --- a/include/raptor/build/raptor_build.hpp +++ b/include/raptor/build/raptor_build.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::raptor_build. diff --git a/include/raptor/build/store_index.hpp b/include/raptor/build/store_index.hpp index ca0acf0b..b6136ea9 100644 --- a/include/raptor/build/store_index.hpp +++ b/include/raptor/build/store_index.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::store_index. diff --git a/include/raptor/call_parallel_on_bins.hpp b/include/raptor/call_parallel_on_bins.hpp index 1004dd97..ca26a5aa 100644 --- a/include/raptor/call_parallel_on_bins.hpp +++ b/include/raptor/call_parallel_on_bins.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::call_parallel_on_bins. diff --git a/include/raptor/dna4_traits.hpp b/include/raptor/dna4_traits.hpp index 8336890c..3423801b 100644 --- a/include/raptor/dna4_traits.hpp +++ b/include/raptor/dna4_traits.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::dna4_traits. diff --git a/include/raptor/file_reader.hpp b/include/raptor/file_reader.hpp index 70535c07..97192f27 100644 --- a/include/raptor/file_reader.hpp +++ b/include/raptor/file_reader.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::file_reader. diff --git a/include/raptor/index.hpp b/include/raptor/index.hpp index 77aba5fe..3ef56a44 100644 --- a/include/raptor/index.hpp +++ b/include/raptor/index.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::raptor_index. diff --git a/include/raptor/layout/raptor_layout.hpp b/include/raptor/layout/raptor_layout.hpp index fc19ceed..2021d13e 100644 --- a/include/raptor/layout/raptor_layout.hpp +++ b/include/raptor/layout/raptor_layout.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::chopper_layout. diff --git a/include/raptor/prepare/compute_minimiser.hpp b/include/raptor/prepare/compute_minimiser.hpp index 1bb3aeeb..8cef2567 100644 --- a/include/raptor/prepare/compute_minimiser.hpp +++ b/include/raptor/prepare/compute_minimiser.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::compute_minimiser. diff --git a/include/raptor/prepare/cutoff.hpp b/include/raptor/prepare/cutoff.hpp index 5151052d..aaa2d975 100644 --- a/include/raptor/prepare/cutoff.hpp +++ b/include/raptor/prepare/cutoff.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::cutoff. diff --git a/include/raptor/raptor.hpp b/include/raptor/raptor.hpp index e61b014d..702a999c 100644 --- a/include/raptor/raptor.hpp +++ b/include/raptor/raptor.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor callable. diff --git a/include/raptor/search/do_parallel.hpp b/include/raptor/search/do_parallel.hpp index 7e128fc9..e1dafc26 100644 --- a/include/raptor/search/do_parallel.hpp +++ b/include/raptor/search/do_parallel.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::do_parallel. diff --git a/include/raptor/search/load_index.hpp b/include/raptor/search/load_index.hpp index 450f5709..4f6ade62 100644 --- a/include/raptor/search/load_index.hpp +++ b/include/raptor/search/load_index.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::load_index. diff --git a/include/raptor/search/search.hpp b/include/raptor/search/search.hpp index e844b8d0..8df58a78 100644 --- a/include/raptor/search/search.hpp +++ b/include/raptor/search/search.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::raptor_search. diff --git a/include/raptor/search/search_hibf.hpp b/include/raptor/search/search_hibf.hpp index e5cbfc49..de438397 100644 --- a/include/raptor/search/search_hibf.hpp +++ b/include/raptor/search/search_hibf.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::search_hibf. diff --git a/include/raptor/search/search_ibf.hpp b/include/raptor/search/search_ibf.hpp index 78185fac..a3323a31 100644 --- a/include/raptor/search/search_ibf.hpp +++ b/include/raptor/search/search_ibf.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::search_ibf. diff --git a/include/raptor/search/search_partitioned_ibf.hpp b/include/raptor/search/search_partitioned_ibf.hpp index 030d30f6..c34461ff 100644 --- a/include/raptor/search/search_partitioned_ibf.hpp +++ b/include/raptor/search/search_partitioned_ibf.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::search_partitioned_ibf. diff --git a/include/raptor/search/search_singular_ibf.hpp b/include/raptor/search/search_singular_ibf.hpp index 361815ee..0bc02b12 100644 --- a/include/raptor/search/search_singular_ibf.hpp +++ b/include/raptor/search/search_singular_ibf.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::search_singular_ibf. diff --git a/include/raptor/search/sync_out.hpp b/include/raptor/search/sync_out.hpp index 2907b861..64782ab2 100644 --- a/include/raptor/search/sync_out.hpp +++ b/include/raptor/search/sync_out.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::sync_out. diff --git a/include/raptor/strong_types.hpp b/include/raptor/strong_types.hpp index 9397a3a5..6fb17fc0 100644 --- a/include/raptor/strong_types.hpp +++ b/include/raptor/strong_types.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::window. diff --git a/include/raptor/threshold/forward_strand_minimiser.hpp b/include/raptor/threshold/forward_strand_minimiser.hpp index 6fc425f7..ea6af8e3 100644 --- a/include/raptor/threshold/forward_strand_minimiser.hpp +++ b/include/raptor/threshold/forward_strand_minimiser.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::threshold::forward_strand_minimiser. diff --git a/include/raptor/threshold/logspace.hpp b/include/raptor/threshold/logspace.hpp index 1f3209fb..1a729b4f 100644 --- a/include/raptor/threshold/logspace.hpp +++ b/include/raptor/threshold/logspace.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides functionality for working with probabilities in logspace. diff --git a/include/raptor/threshold/multiple_error_model.hpp b/include/raptor/threshold/multiple_error_model.hpp index 6b3a7154..58435cfb 100644 --- a/include/raptor/threshold/multiple_error_model.hpp +++ b/include/raptor/threshold/multiple_error_model.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::threshold::multiple_error_model. diff --git a/include/raptor/threshold/one_error_model.hpp b/include/raptor/threshold/one_error_model.hpp index ff2078a0..1fe9dab1 100644 --- a/include/raptor/threshold/one_error_model.hpp +++ b/include/raptor/threshold/one_error_model.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::threshold::one_error_model. diff --git a/include/raptor/threshold/one_indirect_error_model.hpp b/include/raptor/threshold/one_indirect_error_model.hpp index e58f620e..76c70d33 100644 --- a/include/raptor/threshold/one_indirect_error_model.hpp +++ b/include/raptor/threshold/one_indirect_error_model.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::threshold::one_indirect_error_model. diff --git a/include/raptor/threshold/pascal_row.hpp b/include/raptor/threshold/pascal_row.hpp index 58bef5a8..b26d3cce 100644 --- a/include/raptor/threshold/pascal_row.hpp +++ b/include/raptor/threshold/pascal_row.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::threshold::pascal_row. diff --git a/include/raptor/threshold/precompute_correction.hpp b/include/raptor/threshold/precompute_correction.hpp index 1f1b83ad..313968d9 100644 --- a/include/raptor/threshold/precompute_correction.hpp +++ b/include/raptor/threshold/precompute_correction.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::threshold::precompute_correction. diff --git a/include/raptor/threshold/precompute_threshold.hpp b/include/raptor/threshold/precompute_threshold.hpp index e3fc1a3b..de4aec0a 100644 --- a/include/raptor/threshold/precompute_threshold.hpp +++ b/include/raptor/threshold/precompute_threshold.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::threshold::precompute_threshold. diff --git a/include/raptor/threshold/threshold.hpp b/include/raptor/threshold/threshold.hpp index 2a06acd1..830e146b 100644 --- a/include/raptor/threshold/threshold.hpp +++ b/include/raptor/threshold/threshold.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::threshold::threshold. diff --git a/include/raptor/threshold/threshold_parameters.hpp b/include/raptor/threshold/threshold_parameters.hpp index 0f4764f3..29fbf703 100644 --- a/include/raptor/threshold/threshold_parameters.hpp +++ b/include/raptor/threshold/threshold_parameters.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::threshold::threshold_parameters. diff --git a/include/raptor/upgrade/index_upgrader.hpp b/include/raptor/upgrade/index_upgrader.hpp index 6f7e3508..3d5c7300 100644 --- a/include/raptor/upgrade/index_upgrader.hpp +++ b/include/raptor/upgrade/index_upgrader.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::index_upgrader. diff --git a/include/raptor/upgrade/upgrade.hpp b/include/raptor/upgrade/upgrade.hpp index 83433904..7f0bc71d 100644 --- a/include/raptor/upgrade/upgrade.hpp +++ b/include/raptor/upgrade/upgrade.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides raptor::raptor_upgrade. diff --git a/include/raptor/version.hpp b/include/raptor/version.hpp index 4cb736b2..088a2acb 100644 --- a/include/raptor/version.hpp +++ b/include/raptor/version.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Provides RAPTOR version macros and global variables. diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index a71704ec..0adde2f1 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + cmake_minimum_required (VERSION 3.25) if (TARGET raptor) diff --git a/src/argument_parsing/CMakeLists.txt b/src/argument_parsing/CMakeLists.txt index 4d326cb1..ac19a5f0 100644 --- a/src/argument_parsing/CMakeLists.txt +++ b/src/argument_parsing/CMakeLists.txt @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + cmake_minimum_required (VERSION 3.25) if (TARGET raptor_argument_parsing) diff --git a/src/argument_parsing/build_arguments.cpp b/src/argument_parsing/build_arguments.cpp index e8f404b9..7776d6d8 100644 --- a/src/argument_parsing/build_arguments.cpp +++ b/src/argument_parsing/build_arguments.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::build_arguments. diff --git a/src/argument_parsing/build_parsing.cpp b/src/argument_parsing/build_parsing.cpp index 54c7fb44..2ce64ba6 100644 --- a/src/argument_parsing/build_parsing.cpp +++ b/src/argument_parsing/build_parsing.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::build_parsing. diff --git a/src/argument_parsing/compute_bin_size.cpp b/src/argument_parsing/compute_bin_size.cpp index e7cd0eb4..5b6ff423 100644 --- a/src/argument_parsing/compute_bin_size.cpp +++ b/src/argument_parsing/compute_bin_size.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::compute_bin_size and raptor::max_bin_count. diff --git a/src/argument_parsing/init_shared_meta.cpp b/src/argument_parsing/init_shared_meta.cpp index 6807f937..68178d61 100644 --- a/src/argument_parsing/init_shared_meta.cpp +++ b/src/argument_parsing/init_shared_meta.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::init_shared_meta. diff --git a/src/argument_parsing/parse_bin_path.cpp b/src/argument_parsing/parse_bin_path.cpp index f97f8a23..2ae8cc77 100644 --- a/src/argument_parsing/parse_bin_path.cpp +++ b/src/argument_parsing/parse_bin_path.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::parse_bin_path. diff --git a/src/argument_parsing/prepare_parsing.cpp b/src/argument_parsing/prepare_parsing.cpp index 651e3629..d6691622 100644 --- a/src/argument_parsing/prepare_parsing.cpp +++ b/src/argument_parsing/prepare_parsing.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::prepare_parsing. diff --git a/src/argument_parsing/search_arguments.cpp b/src/argument_parsing/search_arguments.cpp index 3358574c..be2e04d5 100644 --- a/src/argument_parsing/search_arguments.cpp +++ b/src/argument_parsing/search_arguments.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::search_arguments. diff --git a/src/argument_parsing/search_parsing.cpp b/src/argument_parsing/search_parsing.cpp index b819a133..55e88e8b 100644 --- a/src/argument_parsing/search_parsing.cpp +++ b/src/argument_parsing/search_parsing.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::search_parsing. diff --git a/src/argument_parsing/upgrade_parsing.cpp b/src/argument_parsing/upgrade_parsing.cpp index c50044b3..41994c1c 100644 --- a/src/argument_parsing/upgrade_parsing.cpp +++ b/src/argument_parsing/upgrade_parsing.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::upgrade_parsing. diff --git a/src/build/CMakeLists.txt b/src/build/CMakeLists.txt index 1889d38d..05c964b6 100644 --- a/src/build/CMakeLists.txt +++ b/src/build/CMakeLists.txt @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + cmake_minimum_required (VERSION 3.25) if (TARGET raptor_build) diff --git a/src/build/build_hibf.cpp b/src/build/build_hibf.cpp index f2ea4736..2823b525 100644 --- a/src/build/build_hibf.cpp +++ b/src/build/build_hibf.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::build_hibf. diff --git a/src/build/build_ibf.cpp b/src/build/build_ibf.cpp index 3031413c..cf9710c8 100644 --- a/src/build/build_ibf.cpp +++ b/src/build/build_ibf.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::build_ibf. diff --git a/src/build/max_count_per_partition.cpp b/src/build/max_count_per_partition.cpp index 66a1c769..c47e04cd 100644 --- a/src/build/max_count_per_partition.cpp +++ b/src/build/max_count_per_partition.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::max_count_per_partition. diff --git a/src/build/raptor_build.cpp b/src/build/raptor_build.cpp index 7ab38d83..c2c5b475 100644 --- a/src/build/raptor_build.cpp +++ b/src/build/raptor_build.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::raptor_build. diff --git a/src/layout/CMakeLists.txt b/src/layout/CMakeLists.txt index 32459c9e..1034c649 100644 --- a/src/layout/CMakeLists.txt +++ b/src/layout/CMakeLists.txt @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + cmake_minimum_required (VERSION 3.15) if (TARGET raptor_layout) diff --git a/src/layout/raptor_layout.cpp b/src/layout/raptor_layout.cpp index a128b535..6292dc48 100644 --- a/src/layout/raptor_layout.cpp +++ b/src/layout/raptor_layout.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::chopper_layout. diff --git a/src/prepare/CMakeLists.txt b/src/prepare/CMakeLists.txt index 428ae3c3..95ac147c 100644 --- a/src/prepare/CMakeLists.txt +++ b/src/prepare/CMakeLists.txt @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + cmake_minimum_required (VERSION 3.25) if (TARGET raptor_prepare) diff --git a/src/prepare/compute_minimiser.cpp b/src/prepare/compute_minimiser.cpp index 8bb21387..7e52298b 100644 --- a/src/prepare/compute_minimiser.cpp +++ b/src/prepare/compute_minimiser.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::compute_minimiser. diff --git a/src/raptor.cpp b/src/raptor.cpp index f57af1a2..8548f5a1 100644 --- a/src/raptor.cpp +++ b/src/raptor.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor. diff --git a/src/search/CMakeLists.txt b/src/search/CMakeLists.txt index 5b3e53c7..f5e79b06 100644 --- a/src/search/CMakeLists.txt +++ b/src/search/CMakeLists.txt @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + cmake_minimum_required (VERSION 3.25) if (TARGET raptor_search) diff --git a/src/search/raptor_search.cpp b/src/search/raptor_search.cpp index 65df04db..1fa4010b 100644 --- a/src/search/raptor_search.cpp +++ b/src/search/raptor_search.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::raptor_search. diff --git a/src/search/search_hibf.cpp b/src/search/search_hibf.cpp index 2944e72d..de101f07 100644 --- a/src/search/search_hibf.cpp +++ b/src/search/search_hibf.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::search_hibf. diff --git a/src/search/search_ibf.cpp b/src/search/search_ibf.cpp index 7d2c635c..feb44643 100644 --- a/src/search/search_ibf.cpp +++ b/src/search/search_ibf.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::search_ibf. diff --git a/src/search/search_partitioned_ibf.cpp b/src/search/search_partitioned_ibf.cpp index bca75e7f..0d506f41 100644 --- a/src/search/search_partitioned_ibf.cpp +++ b/src/search/search_partitioned_ibf.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::search_partitioned_ibf. diff --git a/src/threshold/CMakeLists.txt b/src/threshold/CMakeLists.txt index 448ce7c4..8a485269 100644 --- a/src/threshold/CMakeLists.txt +++ b/src/threshold/CMakeLists.txt @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + cmake_minimum_required (VERSION 3.25) if (TARGET raptor_threshold) diff --git a/src/threshold/multiple_error_model.cpp b/src/threshold/multiple_error_model.cpp index 275854f1..3fcf80bb 100644 --- a/src/threshold/multiple_error_model.cpp +++ b/src/threshold/multiple_error_model.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::threshold::multiple_error_model. diff --git a/src/threshold/one_error_model.cpp b/src/threshold/one_error_model.cpp index f5a25d3c..5b91b742 100644 --- a/src/threshold/one_error_model.cpp +++ b/src/threshold/one_error_model.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::threshold::one_error_model. diff --git a/src/threshold/one_indirect_error_model.cpp b/src/threshold/one_indirect_error_model.cpp index 992c41e1..b02fec0c 100644 --- a/src/threshold/one_indirect_error_model.cpp +++ b/src/threshold/one_indirect_error_model.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::threshold::one_indirect_error_model. diff --git a/src/threshold/pascal_row.cpp b/src/threshold/pascal_row.cpp index 08c5c01c..a5edfa9f 100644 --- a/src/threshold/pascal_row.cpp +++ b/src/threshold/pascal_row.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::threshold::pascal_row. diff --git a/src/threshold/precompute_correction.cpp b/src/threshold/precompute_correction.cpp index 287cbdd7..e78faa70 100644 --- a/src/threshold/precompute_correction.cpp +++ b/src/threshold/precompute_correction.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::threshold::precompute_correction. diff --git a/src/threshold/precompute_threshold.cpp b/src/threshold/precompute_threshold.cpp index 369aab26..85bf1d04 100644 --- a/src/threshold/precompute_threshold.cpp +++ b/src/threshold/precompute_threshold.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::threshold::precompute_threshold. diff --git a/src/threshold/threshold.cpp b/src/threshold/threshold.cpp index 1d57418c..5c388c89 100644 --- a/src/threshold/threshold.cpp +++ b/src/threshold/threshold.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::threshold::threshold. diff --git a/src/upgrade/CMakeLists.txt b/src/upgrade/CMakeLists.txt index a10c0e63..9b2db3a5 100644 --- a/src/upgrade/CMakeLists.txt +++ b/src/upgrade/CMakeLists.txt @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + cmake_minimum_required (VERSION 3.25) if (TARGET raptor_upgrade) diff --git a/src/upgrade/raptor_upgrade.cpp b/src/upgrade/raptor_upgrade.cpp index afb7f352..8a915b7f 100644 --- a/src/upgrade/raptor_upgrade.cpp +++ b/src/upgrade/raptor_upgrade.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \brief Implements raptor::raptor_upgrade. diff --git a/test/cmake/app_datasources.cmake b/test/cmake/app_datasources.cmake index d8361848..09c1537d 100644 --- a/test/cmake/app_datasources.cmake +++ b/test/cmake/app_datasources.cmake @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + include (ExternalProject) # Example call: diff --git a/test/cmake/app_internal_datasources.cmake b/test/cmake/app_internal_datasources.cmake index ae30ed37..ea77b305 100644 --- a/test/cmake/app_internal_datasources.cmake +++ b/test/cmake/app_internal_datasources.cmake @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + # Options: # # declare_internal_datasource (FILE URL URL_HASH = CONFIGURE ) diff --git a/test/cmake/raptor_add_benchmark.cmake b/test/cmake/raptor_add_benchmark.cmake index 3a9702a7..c865f77a 100644 --- a/test/cmake/raptor_add_benchmark.cmake +++ b/test/cmake/raptor_add_benchmark.cmake @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause # A macro that adds a benchmark. macro (raptor_add_benchmark test_filename) diff --git a/test/cmake/raptor_add_unit_test.cmake b/test/cmake/raptor_add_unit_test.cmake index 8c1a6f12..55e3c3a2 100644 --- a/test/cmake/raptor_add_unit_test.cmake +++ b/test/cmake/raptor_add_unit_test.cmake @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause # A macro that adds an api or cli test. macro (raptor_add_unit_test test_filename) diff --git a/test/cmake/raptor_path_longest_stem.cmake b/test/cmake/raptor_path_longest_stem.cmake index c8c8b4f8..27c983ac 100644 --- a/test/cmake/raptor_path_longest_stem.cmake +++ b/test/cmake/raptor_path_longest_stem.cmake @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/test/cmake/raptor_test_component.cmake b/test/cmake/raptor_test_component.cmake index e8555b4b..18c76028 100644 --- a/test/cmake/raptor_test_component.cmake +++ b/test/cmake/raptor_test_component.cmake @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/test/cmake/raptor_test_files.cmake b/test/cmake/raptor_test_files.cmake index 27b62091..c2044447 100644 --- a/test/cmake/raptor_test_files.cmake +++ b/test/cmake/raptor_test_files.cmake @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.17) diff --git a/test/coverage/CMakeLists.txt b/test/coverage/CMakeLists.txt index 2db4e5c1..87c214e9 100644 --- a/test/coverage/CMakeLists.txt +++ b/test/coverage/CMakeLists.txt @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/test/coverage/README.md b/test/coverage/README.md index 12742ea3..f015d0a0 100644 --- a/test/coverage/README.md +++ b/test/coverage/README.md @@ -1,3 +1,9 @@ + + # Coverage Test This is the test for the code coverage. diff --git a/test/documentation/.vercel/0_setup.sh b/test/documentation/.vercel/0_setup.sh index f0824b20..664bca22 100755 --- a/test/documentation/.vercel/0_setup.sh +++ b/test/documentation/.vercel/0_setup.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -euxo pipefail DOXYGEN_VERSION=1.9.6 diff --git a/test/documentation/.vercel/1_build.sh b/test/documentation/.vercel/1_build.sh index 332c09ff..d21809fa 100755 --- a/test/documentation/.vercel/1_build.sh +++ b/test/documentation/.vercel/1_build.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -euxo pipefail WORK_DIR=`pwd` diff --git a/test/documentation/.vercel/Notes.md b/test/documentation/.vercel/Notes.md index 1d7c365a..093e4293 100644 --- a/test/documentation/.vercel/Notes.md +++ b/test/documentation/.vercel/Notes.md @@ -1,3 +1,9 @@ + + * Framekwork: Other * Build Command: ./1_build.sh * Output Directory: ./export/html diff --git a/test/documentation/.vercel/api/doxysearch.sh b/test/documentation/.vercel/api/doxysearch.sh index 8d29de76..05d5cd25 100644 --- a/test/documentation/.vercel/api/doxysearch.sh +++ b/test/documentation/.vercel/api/doxysearch.sh @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + import "querystring@1.3.0" build() { diff --git a/test/documentation/.vercel/powered-by-vercel.svg.license b/test/documentation/.vercel/powered-by-vercel.svg.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/test/documentation/.vercel/powered-by-vercel.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/test/documentation/.vercel/vercel.json.license b/test/documentation/.vercel/vercel.json.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/test/documentation/.vercel/vercel.json.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/test/documentation/CMakeLists.txt b/test/documentation/CMakeLists.txt index 2aaae147..61fb6bee 100644 --- a/test/documentation/CMakeLists.txt +++ b/test/documentation/CMakeLists.txt @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause # Minimum cmake version cmake_minimum_required (VERSION 3.17) diff --git a/test/documentation/DoxygenLayout.xml b/test/documentation/DoxygenLayout.xml index afa5543a..ceeaf438 100644 --- a/test/documentation/DoxygenLayout.xml +++ b/test/documentation/DoxygenLayout.xml @@ -1,3 +1,9 @@ + + diff --git a/test/documentation/README.md b/test/documentation/README.md index 9ed4a0b1..69893634 100644 --- a/test/documentation/README.md +++ b/test/documentation/README.md @@ -1,3 +1,9 @@ + + # raptor documentation Currently, we can only build the documentation on *nix systems. diff --git a/test/documentation/doxygen-awesome/doxygen-awesome-darkmode-toggle.js b/test/documentation/doxygen-awesome/doxygen-awesome-darkmode-toggle.js index 40fe2d38..3e7ba3f3 100644 --- a/test/documentation/doxygen-awesome/doxygen-awesome-darkmode-toggle.js +++ b/test/documentation/doxygen-awesome/doxygen-awesome-darkmode-toggle.js @@ -1,3 +1,6 @@ +// SPDX-FileCopyrightText: 2023 2021 - 2023 jothepro +// SPDX-License-Identifier: MIT + /** Doxygen Awesome @@ -46,7 +49,7 @@ class DoxygenAwesomeDarkModeToggle extends HTMLElement { DoxygenAwesomeDarkModeToggle.onSystemPreferenceChanged() }) // Update the color scheme when the tab is made visible again. - // It is possible that the appearance was changed in another tab + // It is possible that the appearance was changed in another tab // while this tab was in the background. document.addEventListener("visibilitychange", visibilityState => { if (document.visibilityState === 'visible') { @@ -97,7 +100,7 @@ class DoxygenAwesomeDarkModeToggle extends HTMLElement { * @returns `true` for dark-mode, `false` for light-mode user preference */ static get userPreference() { - return (!DoxygenAwesomeDarkModeToggle.systemPreference && localStorage.getItem(DoxygenAwesomeDarkModeToggle.prefersDarkModeInLightModeKey)) || + return (!DoxygenAwesomeDarkModeToggle.systemPreference && localStorage.getItem(DoxygenAwesomeDarkModeToggle.prefersDarkModeInLightModeKey)) || (DoxygenAwesomeDarkModeToggle.systemPreference && !localStorage.getItem(DoxygenAwesomeDarkModeToggle.prefersLightModeInDarkModeKey)) } diff --git a/test/documentation/doxygen-awesome/doxygen-awesome-fragment-copy-button.js b/test/documentation/doxygen-awesome/doxygen-awesome-fragment-copy-button.js index 86c16fd9..c0cd50aa 100644 --- a/test/documentation/doxygen-awesome/doxygen-awesome-fragment-copy-button.js +++ b/test/documentation/doxygen-awesome/doxygen-awesome-fragment-copy-button.js @@ -1,3 +1,6 @@ +// SPDX-FileCopyrightText: 2023 2021 - 2023 jothepro +// SPDX-License-Identifier: MIT + /** Doxygen Awesome @@ -47,11 +50,11 @@ class DoxygenAwesomeFragmentCopyButton extends HTMLElement { const fragmentCopyButton = document.createElement("doxygen-awesome-fragment-copy-button") fragmentCopyButton.innerHTML = DoxygenAwesomeFragmentCopyButton.copyIcon fragmentCopyButton.title = DoxygenAwesomeFragmentCopyButton.title - + fragment.parentNode.replaceChild(fragmentWrapper, fragment) fragmentWrapper.appendChild(fragment) fragmentWrapper.appendChild(fragmentCopyButton) - + } } }) diff --git a/test/documentation/doxygen-awesome/doxygen-awesome-interactive-toc.js b/test/documentation/doxygen-awesome/doxygen-awesome-interactive-toc.js index 20a9669d..ca7f17d5 100644 --- a/test/documentation/doxygen-awesome/doxygen-awesome-interactive-toc.js +++ b/test/documentation/doxygen-awesome/doxygen-awesome-interactive-toc.js @@ -1,3 +1,6 @@ +// SPDX-FileCopyrightText: 2023 2021 - 2023 jothepro +// SPDX-License-Identifier: MIT + /** Doxygen Awesome @@ -78,4 +81,4 @@ class DoxygenAwesomeInteractiveToc { active?.classList.add("active") active?.classList.remove("aboveActive") } -} \ No newline at end of file +} diff --git a/test/documentation/doxygen-awesome/doxygen-awesome-paragraph-link.js b/test/documentation/doxygen-awesome/doxygen-awesome-paragraph-link.js index e53d132c..e8c7b1ff 100644 --- a/test/documentation/doxygen-awesome/doxygen-awesome-paragraph-link.js +++ b/test/documentation/doxygen-awesome/doxygen-awesome-paragraph-link.js @@ -1,3 +1,6 @@ +// SPDX-FileCopyrightText: 2023 2021 - 2023 jothepro +// SPDX-License-Identifier: MIT + /** Doxygen Awesome diff --git a/test/documentation/doxygen-awesome/doxygen-awesome-sidebar-only-darkmode-toggle.css b/test/documentation/doxygen-awesome/doxygen-awesome-sidebar-only-darkmode-toggle.css index d207446e..018a647d 100644 --- a/test/documentation/doxygen-awesome/doxygen-awesome-sidebar-only-darkmode-toggle.css +++ b/test/documentation/doxygen-awesome/doxygen-awesome-sidebar-only-darkmode-toggle.css @@ -1,3 +1,7 @@ +/* + * SPDX-FileCopyrightText: 2023 2021 - 2023 jothepro + * SPDX-License-Identifier: MIT + */ /** diff --git a/test/documentation/doxygen-awesome/doxygen-awesome-sidebar-only.css b/test/documentation/doxygen-awesome/doxygen-awesome-sidebar-only.css index 84356cd5..33e3d668 100644 --- a/test/documentation/doxygen-awesome/doxygen-awesome-sidebar-only.css +++ b/test/documentation/doxygen-awesome/doxygen-awesome-sidebar-only.css @@ -1,3 +1,8 @@ +/* + * SPDX-FileCopyrightText: 2023 2021 - 2023 jothepro + * SPDX-License-Identifier: MIT + */ + /** Doxygen Awesome diff --git a/test/documentation/doxygen-awesome/doxygen-awesome-tabs.js b/test/documentation/doxygen-awesome/doxygen-awesome-tabs.js index 8e725b23..80949e05 100644 --- a/test/documentation/doxygen-awesome/doxygen-awesome-tabs.js +++ b/test/documentation/doxygen-awesome/doxygen-awesome-tabs.js @@ -1,3 +1,6 @@ +// SPDX-FileCopyrightText: 2023 2021 - 2023 jothepro +// SPDX-License-Identifier: MIT + /** Doxygen Awesome @@ -67,4 +70,4 @@ class DoxygenAwesomeTabs { }) }) } -} \ No newline at end of file +} diff --git a/test/documentation/doxygen-awesome/doxygen-awesome.css b/test/documentation/doxygen-awesome/doxygen-awesome.css index e8399cbc..a07f389d 100644 --- a/test/documentation/doxygen-awesome/doxygen-awesome.css +++ b/test/documentation/doxygen-awesome/doxygen-awesome.css @@ -1,3 +1,8 @@ +/* + * SPDX-FileCopyrightText: 2023 2021 - 2023 jothepro + * SPDX-License-Identifier: MIT + */ + /** Doxygen Awesome @@ -204,7 +209,7 @@ html { --code-background: #2a2c2f; --tablehead-background: #2a2c2f; - + --blockquote-background: #222325; --blockquote-foreground: #7e8c92; @@ -885,7 +890,7 @@ div.header { flex-wrap: nowrap; align-items: flex-start; } - + div.contents .textblock { min-width: 200px; flex-grow: 1; @@ -977,21 +982,21 @@ html.dark-mode div.contents .dotgraph iframe h2.groupheader { border-bottom: 0px; color: var(--page-foreground-color); - box-shadow: - 100px 0 var(--page-background-color), + box-shadow: + 100px 0 var(--page-background-color), -100px 0 var(--page-background-color), 100px 0.75px var(--separator-color), -100px 0.75px var(--separator-color), - 500px 0 var(--page-background-color), + 500px 0 var(--page-background-color), -500px 0 var(--page-background-color), 500px 0.75px var(--separator-color), -500px 0.75px var(--separator-color), - 900px 0 var(--page-background-color), + 900px 0 var(--page-background-color), -900px 0 var(--page-background-color), 900px 0.75px var(--separator-color), -900px 0.75px var(--separator-color), 1400px 0 var(--page-background-color), - -1400px 0 var(--page-background-color), + -1400px 0 var(--page-background-color), 1400px 0.75px var(--separator-color), -1400px 0.75px var(--separator-color), 1900px 0 var(--page-background-color), @@ -1162,8 +1167,8 @@ div.toc li a.aboveActive { div.contents .toc.interactive > h3::before { content: ""; - width: 0; - height: 0; + width: 0; + height: 0; border-left: 4px solid transparent; border-right: 4px solid transparent; border-top: 5px solid var(--primary-color); @@ -1854,8 +1859,8 @@ table.memberdecls img[src="closed.png"], table.memberdecls img[src="open.png"], div.dynheader img[src="open.png"], div.dynheader img[src="closed.png"] { - width: 0; - height: 0; + width: 0; + height: 0; border-left: 4px solid transparent; border-right: 4px solid transparent; border-top: 5px solid var(--primary-color); @@ -1873,7 +1878,7 @@ table.memberdecls img { table.memberdecls img[src="closed.png"], div.dynheader img[src="closed.png"] { transform: rotate(-90deg); - + } .compoundTemplParams { @@ -1916,7 +1921,7 @@ div.dynheader img[src="closed.png"] { margin-bottom: calc(0px - var(--page-font-size)); } - table.memberdecls .memItemRight, + table.memberdecls .memItemRight, table.memberdecls .mdescRight, table.memberdecls .memTemplItemRight { border-top: 0; @@ -2102,8 +2107,8 @@ html.dark-mode .iconfopen, html.dark-mode .iconfclosed { background-color: transparent; } -/* - Class Index Doxygen 1.8 +/* + Class Index Doxygen 1.8 */ table.classindex { @@ -2248,7 +2253,7 @@ div.contents .toc::-webkit-scrollbar-thumb, background-color: transparent; border: var(--webkit-scrollbar-padding) solid transparent; border-radius: calc(var(--webkit-scrollbar-padding) + var(--webkit-scrollbar-padding)); - background-clip: padding-box; + background-clip: padding-box; } #nav-tree:hover::-webkit-scrollbar-thumb, @@ -2519,4 +2524,4 @@ h2:hover a.anchorlink, h1:hover a.anchorlink, h3:hover a.anchorlink, h4:hover a. html.dark-mode .tabs-overview button.tab-button:hover .tab-title { color: var(--page-foreground-color); -} \ No newline at end of file +} diff --git a/test/documentation/raptor-doxygen-layout.cmake b/test/documentation/raptor-doxygen-layout.cmake index fb0d51c8..1f0f16a2 100644 --- a/test/documentation/raptor-doxygen-layout.cmake +++ b/test/documentation/raptor-doxygen-layout.cmake @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.17) diff --git a/test/documentation/raptor-doxygen.cmake b/test/documentation/raptor-doxygen.cmake index 79506bba..01309cf4 100644 --- a/test/documentation/raptor-doxygen.cmake +++ b/test/documentation/raptor-doxygen.cmake @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.17) diff --git a/test/documentation/raptor_doxygen_cfg.in b/test/documentation/raptor_doxygen_cfg.in index e0971ec4..315de687 100644 --- a/test/documentation/raptor_doxygen_cfg.in +++ b/test/documentation/raptor_doxygen_cfg.in @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024, Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + # Doxyfile 1.9.6 #--------------------------------------------------------------------------- diff --git a/test/documentation/raptor_footer.html.in b/test/documentation/raptor_footer.html.in index 209dbc38..e6f88222 100644 --- a/test/documentation/raptor_footer.html.in +++ b/test/documentation/raptor_footer.html.in @@ -1,3 +1,9 @@ + + diff --git a/test/documentation/raptor_header.html b/test/documentation/raptor_header.html index 58a75dbf..9cb7f04b 100644 --- a/test/documentation/raptor_header.html +++ b/test/documentation/raptor_header.html @@ -1,3 +1,9 @@ + + diff --git a/test/header/CMakeLists.txt b/test/header/CMakeLists.txt index 16fe991a..2fd7a036 100644 --- a/test/header/CMakeLists.txt +++ b/test/header/CMakeLists.txt @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/test/include/raptor/test/cli_test.hpp b/test/include/raptor/test/cli_test.hpp index 306629c3..703f49af 100644 --- a/test/include/raptor/test/cli_test.hpp +++ b/test/include/raptor/test/cli_test.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once diff --git a/test/include/raptor/test/tmp_test_file.hpp b/test/include/raptor/test/tmp_test_file.hpp index 0827855b..f1a15308 100644 --- a/test/include/raptor/test/tmp_test_file.hpp +++ b/test/include/raptor/test/tmp_test_file.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once diff --git a/test/performance/CMakeLists.txt b/test/performance/CMakeLists.txt index 886ff2d4..041af947 100644 --- a/test/performance/CMakeLists.txt +++ b/test/performance/CMakeLists.txt @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/test/performance/README.md b/test/performance/README.md index b495e299..b28dad00 100644 --- a/test/performance/README.md +++ b/test/performance/README.md @@ -1,3 +1,9 @@ + + # Benchmarks Here are test files for benchmarks with respect to time, space consumption and memory. diff --git a/test/performance/bin_influence_benchmark.cpp b/test/performance/bin_influence_benchmark.cpp index 86aa64a0..b7921a54 100644 --- a/test/performance/bin_influence_benchmark.cpp +++ b/test/performance/bin_influence_benchmark.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/test/performance/parse.py b/test/performance/parse.py index 676f8812..9ba58458 100644 --- a/test/performance/parse.py +++ b/test/performance/parse.py @@ -1,10 +1,9 @@ #!/usr/bin/env python3 -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + # # Usage parse.py # diff --git a/test/raptor-test.cmake b/test/raptor-test.cmake index e2ab2a2b..acecca14 100644 --- a/test/raptor-test.cmake +++ b/test/raptor-test.cmake @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/test/snippet/CMakeLists.txt b/test/snippet/CMakeLists.txt index 214f8000..31c1ad78 100644 --- a/test/snippet/CMakeLists.txt +++ b/test/snippet/CMakeLists.txt @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) project (raptor_test_snippet LANGUAGES CXX C) diff --git a/test/snippet/compare_snippet_output.cmake b/test/snippet/compare_snippet_output.cmake index 82358a46..c68113bb 100644 --- a/test/snippet/compare_snippet_output.cmake +++ b/test/snippet/compare_snippet_output.cmake @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/test/snippet/snippet_main.cpp b/test/snippet/snippet_main.cpp index 905869df..2e0069cd 100644 --- a/test/snippet/snippet_main.cpp +++ b/test/snippet/snippet_main.cpp @@ -1,3 +1,7 @@ +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause + int main() { return 0; diff --git a/test/unit/CMakeLists.txt b/test/unit/CMakeLists.txt index cf2188a6..a96ba7dc 100644 --- a/test/unit/CMakeLists.txt +++ b/test/unit/CMakeLists.txt @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/test/unit/api/CMakeLists.txt b/test/unit/api/CMakeLists.txt index 5653ed90..c98e7018 100644 --- a/test/unit/api/CMakeLists.txt +++ b/test/unit/api/CMakeLists.txt @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/test/unit/api/formatted_bytes.cpp b/test/unit/api/formatted_bytes.cpp index ef45a88c..3c07c4e4 100644 --- a/test/unit/api/formatted_bytes.cpp +++ b/test/unit/api/formatted_bytes.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/test/unit/api/index_size.cpp b/test/unit/api/index_size.cpp index d978997c..e7ec88bb 100644 --- a/test/unit/api/index_size.cpp +++ b/test/unit/api/index_size.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/test/unit/api/issue_142.cpp b/test/unit/api/issue_142.cpp index 7121f3a9..5a307112 100644 --- a/test/unit/api/issue_142.cpp +++ b/test/unit/api/issue_142.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/test/unit/api/memory_usage.cpp b/test/unit/api/memory_usage.cpp index d815153e..057ae6e1 100644 --- a/test/unit/api/memory_usage.cpp +++ b/test/unit/api/memory_usage.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/test/unit/api/threshold.cpp b/test/unit/api/threshold.cpp index 0c6be7f2..637c5563 100644 --- a/test/unit/api/threshold.cpp +++ b/test/unit/api/threshold.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/test/unit/api/validate_shape.cpp b/test/unit/api/validate_shape.cpp index 25a10411..48ae578b 100644 --- a/test/unit/api/validate_shape.cpp +++ b/test/unit/api/validate_shape.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/test/unit/cli/CMakeLists.txt b/test/unit/cli/CMakeLists.txt index 50de2758..9b841062 100644 --- a/test/unit/cli/CMakeLists.txt +++ b/test/unit/cli/CMakeLists.txt @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/test/unit/cli/argument_parsing/CMakeLists.txt b/test/unit/cli/argument_parsing/CMakeLists.txt index e82fc358..2ad98dc5 100644 --- a/test/unit/cli/argument_parsing/CMakeLists.txt +++ b/test/unit/cli/argument_parsing/CMakeLists.txt @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/test/unit/cli/argument_parsing/options_test.cpp b/test/unit/cli/argument_parsing/options_test.cpp index 40fa3ea9..039180e6 100644 --- a/test/unit/cli/argument_parsing/options_test.cpp +++ b/test/unit/cli/argument_parsing/options_test.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/test/unit/cli/build/CMakeLists.txt b/test/unit/cli/build/CMakeLists.txt index d3acd170..e6e369ea 100644 --- a/test/unit/cli/build/CMakeLists.txt +++ b/test/unit/cli/build/CMakeLists.txt @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/test/unit/cli/build/build_hibf_chopper_test.cpp b/test/unit/cli/build/build_hibf_chopper_test.cpp index c72842dd..c2032642 100644 --- a/test/unit/cli/build/build_hibf_chopper_test.cpp +++ b/test/unit/cli/build/build_hibf_chopper_test.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/test/unit/cli/build/build_hibf_test.cpp b/test/unit/cli/build/build_hibf_test.cpp index 008a37b4..70567966 100644 --- a/test/unit/cli/build/build_hibf_test.cpp +++ b/test/unit/cli/build/build_hibf_test.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/test/unit/cli/build/build_ibf_partitioned_test.cpp b/test/unit/cli/build/build_ibf_partitioned_test.cpp index 425a4b0c..4c0961ea 100644 --- a/test/unit/cli/build/build_ibf_partitioned_test.cpp +++ b/test/unit/cli/build/build_ibf_partitioned_test.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/test/unit/cli/build/build_ibf_test.cpp b/test/unit/cli/build/build_ibf_test.cpp index 255b1179..d39fd8ee 100644 --- a/test/unit/cli/build/build_ibf_test.cpp +++ b/test/unit/cli/build/build_ibf_test.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/test/unit/cli/search/CMakeLists.txt b/test/unit/cli/search/CMakeLists.txt index fdc6e075..7f55a189 100644 --- a/test/unit/cli/search/CMakeLists.txt +++ b/test/unit/cli/search/CMakeLists.txt @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/test/unit/cli/search/search_hibf_preprocessing_test.cpp b/test/unit/cli/search/search_hibf_preprocessing_test.cpp index c7657a27..3e579b62 100644 --- a/test/unit/cli/search/search_hibf_preprocessing_test.cpp +++ b/test/unit/cli/search/search_hibf_preprocessing_test.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/test/unit/cli/search/search_hibf_test.cpp b/test/unit/cli/search/search_hibf_test.cpp index d2bbde82..50dd2289 100644 --- a/test/unit/cli/search/search_hibf_test.cpp +++ b/test/unit/cli/search/search_hibf_test.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/test/unit/cli/search/search_ibf_preprocessing_test.cpp b/test/unit/cli/search/search_ibf_preprocessing_test.cpp index 51a6f2c5..9d4b1735 100644 --- a/test/unit/cli/search/search_ibf_preprocessing_test.cpp +++ b/test/unit/cli/search/search_ibf_preprocessing_test.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/test/unit/cli/search/search_ibf_test.cpp b/test/unit/cli/search/search_ibf_test.cpp index 0355abe4..babae25d 100644 --- a/test/unit/cli/search/search_ibf_test.cpp +++ b/test/unit/cli/search/search_ibf_test.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/test/unit/cli/upgrade/CMakeLists.txt b/test/unit/cli/upgrade/CMakeLists.txt index 63befa33..7a017e9a 100644 --- a/test/unit/cli/upgrade/CMakeLists.txt +++ b/test/unit/cli/upgrade/CMakeLists.txt @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/test/unit/cli/upgrade/upgrade_test.cpp b/test/unit/cli/upgrade/upgrade_test.cpp index 16746f6d..c514332a 100644 --- a/test/unit/cli/upgrade/upgrade_test.cpp +++ b/test/unit/cli/upgrade/upgrade_test.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/test/util/collect_compile_stats.sh b/test/util/collect_compile_stats.sh index 76a5a9cb..0d4e1cd8 100755 --- a/test/util/collect_compile_stats.sh +++ b/test/util/collect_compile_stats.sh @@ -1,10 +1,9 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + # # Usage: collect_compile_stats.sh # Will compile the project in the current working directory and create a summary of compile time and memory usage per diff --git a/test/util/g++.sh b/test/util/g++.sh index fe752bd1..5c30dcef 100755 --- a/test/util/g++.sh +++ b/test/util/g++.sh @@ -1,5 +1,9 @@ #!/usr/bin/env bash +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + GCC="/usr/bin/g++-11" DO_TIME=0 diff --git a/test/util/gcc.sh b/test/util/gcc.sh index 98d31022..6f76316e 100755 --- a/test/util/gcc.sh +++ b/test/util/gcc.sh @@ -1,5 +1,9 @@ #!/usr/bin/env bash +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + GCC="/usr/bin/gcc-11" DO_TIME=0 diff --git a/test/util/link_check.sh b/test/util/link_check.sh index 14eec3cc..0b161579 100755 --- a/test/util/link_check.sh +++ b/test/util/link_check.sh @@ -1,10 +1,9 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + # # Usage: link_check.sh # Will output the status of links in the repository. diff --git a/test/util/ram_usage.py b/test/util/ram_usage.py index 036cf95b..6299d5ea 100755 --- a/test/util/ram_usage.py +++ b/test/util/ram_usage.py @@ -1,10 +1,9 @@ #!/usr/bin/env python3 -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + # # Usage ram_usage.py # diff --git a/util/Genome_Biology/README.md b/util/Genome_Biology/README.md index eaf0945b..fe5c7f75 100644 --- a/util/Genome_Biology/README.md +++ b/util/Genome_Biology/README.md @@ -1,3 +1,9 @@ + + # :construction: Work in progress :construction: ## Data diff --git a/util/Genome_Biology/benchmark.variables.license b/util/Genome_Biology/benchmark.variables.license new file mode 100644 index 00000000..70b01de1 --- /dev/null +++ b/util/Genome_Biology/benchmark.variables.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: CC-BY-4.0 diff --git a/util/Genome_Biology/bifrost_scripts/bifrost_build.sh b/util/Genome_Biology/bifrost_scripts/bifrost_build.sh index 8d8a6fa1..9cf36e19 100755 --- a/util/Genome_Biology/bifrost_scripts/bifrost_build.sh +++ b/util/Genome_Biology/bifrost_scripts/bifrost_build.sh @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + source /project/archive-index-data/smehringer/benchmark.variables BIF_DIR="${WORKDIR}/bifrost_bench" diff --git a/util/Genome_Biology/bifrost_scripts/bifrost_query.sh b/util/Genome_Biology/bifrost_scripts/bifrost_query.sh index f510b590..6a02a45a 100755 --- a/util/Genome_Biology/bifrost_scripts/bifrost_query.sh +++ b/util/Genome_Biology/bifrost_scripts/bifrost_query.sh @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + source /project/archive-index-data/smehringer/benchmark.variables BIF_DIR="${WORKDIR}/bifrost_bench" diff --git a/util/Genome_Biology/cobs_scripts/COBS_build.sh b/util/Genome_Biology/cobs_scripts/COBS_build.sh index 9ba56ef2..c6ed5168 100755 --- a/util/Genome_Biology/cobs_scripts/COBS_build.sh +++ b/util/Genome_Biology/cobs_scripts/COBS_build.sh @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + source /project/archive-index-data/smehringer/benchmark.variables COBS_DIR="${WORKDIR}/COBS_compact_bench" diff --git a/util/Genome_Biology/cobs_scripts/COBS_query.sh b/util/Genome_Biology/cobs_scripts/COBS_query.sh index c2c65c94..c0361dcb 100755 --- a/util/Genome_Biology/cobs_scripts/COBS_query.sh +++ b/util/Genome_Biology/cobs_scripts/COBS_query.sh @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + source /project/archive-index-data/smehringer/benchmark.variables COBS_DIR="${WORKDIR}/COBS_compact_bench" diff --git a/util/Genome_Biology/hibf_scripts/hibf_build.sh b/util/Genome_Biology/hibf_scripts/hibf_build.sh index 35bdda35..3e3d061f 100755 --- a/util/Genome_Biology/hibf_scripts/hibf_build.sh +++ b/util/Genome_Biology/hibf_scripts/hibf_build.sh @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + source /project/archive-index-data/smehringer/benchmark.variables RAPTOR_DIR="${WORKDIR}/raptor_bench_new" diff --git a/util/Genome_Biology/hibf_scripts/hibf_query.sh b/util/Genome_Biology/hibf_scripts/hibf_query.sh index f4ded5cf..5fb6b4ba 100755 --- a/util/Genome_Biology/hibf_scripts/hibf_query.sh +++ b/util/Genome_Biology/hibf_scripts/hibf_query.sh @@ -1,5 +1,9 @@ #!/bin/bash +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + source /project/archive-index-data/smehringer/benchmark.variables RAPTOR_DIR="${WORKDIR}/raptor_bench_new" diff --git a/util/Genome_Biology/howdesbt_scripts/call_makebf.sh b/util/Genome_Biology/howdesbt_scripts/call_makebf.sh index c6d8482e..d90479a1 100755 --- a/util/Genome_Biology/howdesbt_scripts/call_makebf.sh +++ b/util/Genome_Biology/howdesbt_scripts/call_makebf.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail source /project/archive-index-data/smehringer/benchmark.variables diff --git a/util/Genome_Biology/howdesbt_scripts/howdesbt_build.sh b/util/Genome_Biology/howdesbt_scripts/howdesbt_build.sh index b216eff6..e5aff2db 100755 --- a/util/Genome_Biology/howdesbt_scripts/howdesbt_build.sh +++ b/util/Genome_Biology/howdesbt_scripts/howdesbt_build.sh @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + source /project/archive-index-data/smehringer/benchmark.variables HOW_DIR="${WORKDIR}/howdesbt_bench" diff --git a/util/Genome_Biology/ibf_scripts/raptor_build.sh b/util/Genome_Biology/ibf_scripts/raptor_build.sh index 8ecdbbcd..28ced1e3 100755 --- a/util/Genome_Biology/ibf_scripts/raptor_build.sh +++ b/util/Genome_Biology/ibf_scripts/raptor_build.sh @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + source /project/archive-index-data/smehringer/benchmark.variables RAPTOR_DIR="${WORKDIR}/ibf_bench" diff --git a/util/Genome_Biology/ibf_scripts/raptor_query.sh b/util/Genome_Biology/ibf_scripts/raptor_query.sh index 3fa633f0..c2e9078e 100755 --- a/util/Genome_Biology/ibf_scripts/raptor_query.sh +++ b/util/Genome_Biology/ibf_scripts/raptor_query.sh @@ -1,5 +1,9 @@ #!/bin/bash +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + source /project/archive-index-data/smehringer/benchmark.variables RAPTOR_DIR="${WORKDIR}/ibf_bench" diff --git a/util/Genome_Biology/kmtricks_scripts/kmtricks_build.sh b/util/Genome_Biology/kmtricks_scripts/kmtricks_build.sh index 75825712..3d943f3b 100755 --- a/util/Genome_Biology/kmtricks_scripts/kmtricks_build.sh +++ b/util/Genome_Biology/kmtricks_scripts/kmtricks_build.sh @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + source /project/archive-index-data/smehringer/benchmark.variables KM_DIR="${WORKDIR}/kmtricks_bench" diff --git a/util/Genome_Biology/kmtricks_scripts/kmtricks_prep.sh b/util/Genome_Biology/kmtricks_scripts/kmtricks_prep.sh index d03deb7c..61de6c3f 100755 --- a/util/Genome_Biology/kmtricks_scripts/kmtricks_prep.sh +++ b/util/Genome_Biology/kmtricks_scripts/kmtricks_prep.sh @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + source /project/archive-index-data/smehringer/benchmark.variables KM_DIR="${WORKDIR}/kmtricks_bench" diff --git a/util/Genome_Biology/kmtricks_scripts/kmtricks_query.sh b/util/Genome_Biology/kmtricks_scripts/kmtricks_query.sh index a9b112ec..716d01d2 100755 --- a/util/Genome_Biology/kmtricks_scripts/kmtricks_query.sh +++ b/util/Genome_Biology/kmtricks_scripts/kmtricks_query.sh @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + source /project/archive-index-data/smehringer/benchmark.variables KM_DIR="${WORKDIR}/kmtricks_bench" diff --git a/util/Genome_Biology/mantis_scripts/complete.sh b/util/Genome_Biology/mantis_scripts/complete.sh index c3d394f1..c8c04f12 100755 --- a/util/Genome_Biology/mantis_scripts/complete.sh +++ b/util/Genome_Biology/mantis_scripts/complete.sh @@ -1,10 +1,8 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause set -e SCRIPT_ROOT=$(dirname $(readlink -f $0)) diff --git a/util/Genome_Biology/mantis_scripts/copy_input.sh b/util/Genome_Biology/mantis_scripts/copy_input.sh index d525eb32..251084f7 100755 --- a/util/Genome_Biology/mantis_scripts/copy_input.sh +++ b/util/Genome_Biology/mantis_scripts/copy_input.sh @@ -1,10 +1,8 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -# shipped with this file and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause set -e SCRIPT_ROOT=$(dirname $(readlink -f $0)) diff --git a/util/Genome_Biology/mantis_scripts/mantis_build.sh b/util/Genome_Biology/mantis_scripts/mantis_build.sh index d83f7f6a..49e1de44 100755 --- a/util/Genome_Biology/mantis_scripts/mantis_build.sh +++ b/util/Genome_Biology/mantis_scripts/mantis_build.sh @@ -1,10 +1,8 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -# shipped with this file and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause set -e SCRIPT_ROOT=$(dirname $(readlink -f $0)) diff --git a/util/Genome_Biology/mantis_scripts/mantis_mst.sh b/util/Genome_Biology/mantis_scripts/mantis_mst.sh index 2316f56a..256addd2 100755 --- a/util/Genome_Biology/mantis_scripts/mantis_mst.sh +++ b/util/Genome_Biology/mantis_scripts/mantis_mst.sh @@ -1,10 +1,8 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -# shipped with this file and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause set -e SCRIPT_ROOT=$(dirname $(readlink -f $0)) diff --git a/util/Genome_Biology/mantis_scripts/mantis_query.sh b/util/Genome_Biology/mantis_scripts/mantis_query.sh index f161dfef..2f1ae655 100755 --- a/util/Genome_Biology/mantis_scripts/mantis_query.sh +++ b/util/Genome_Biology/mantis_scripts/mantis_query.sh @@ -1,10 +1,8 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -# shipped with this file and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause set -e SCRIPT_ROOT=$(dirname $(readlink -f $0)) diff --git a/util/Genome_Biology/mantis_scripts/mantis_refseq_query.sh b/util/Genome_Biology/mantis_scripts/mantis_refseq_query.sh index 674173b6..334ba988 100755 --- a/util/Genome_Biology/mantis_scripts/mantis_refseq_query.sh +++ b/util/Genome_Biology/mantis_scripts/mantis_refseq_query.sh @@ -1,10 +1,8 @@ #!/usr/bin/env bash -# ----------------------------------------------------------------------------------------------------- -# Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin -# Copyright (c) 2016-2021, 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/raptor/blob/master/LICENSE.md -# ----------------------------------------------------------------------------------------------------- + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause source /project/archive-index-data/smehringer/benchmark.variables diff --git a/util/Genome_Biology/mantis_scripts/squeakr.sh b/util/Genome_Biology/mantis_scripts/squeakr.sh index fcf295d8..e948adc4 100755 --- a/util/Genome_Biology/mantis_scripts/squeakr.sh +++ b/util/Genome_Biology/mantis_scripts/squeakr.sh @@ -1,10 +1,8 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause set -e SCRIPT_ROOT=$(dirname $(readlink -f $0)) diff --git a/util/Genome_Biology/mantis_scripts/variables.sh b/util/Genome_Biology/mantis_scripts/variables.sh index 591bb66d..cf89fcbe 100755 --- a/util/Genome_Biology/mantis_scripts/variables.sh +++ b/util/Genome_Biology/mantis_scripts/variables.sh @@ -1,10 +1,8 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -# shipped with this file and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause set -e diff --git a/util/Genome_Biology/metagraph_scripts/metagraph_annotate.sh b/util/Genome_Biology/metagraph_scripts/metagraph_annotate.sh index 5ebb04a7..9609b0cc 100755 --- a/util/Genome_Biology/metagraph_scripts/metagraph_annotate.sh +++ b/util/Genome_Biology/metagraph_scripts/metagraph_annotate.sh @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + source /project/archive-index-data/smehringer/benchmark.variables META_DIR="${WORKDIR}/metagraph_bench" diff --git a/util/Genome_Biology/metagraph_scripts/metagraph_build.sh b/util/Genome_Biology/metagraph_scripts/metagraph_build.sh index e38ba3cc..d0d6a51b 100755 --- a/util/Genome_Biology/metagraph_scripts/metagraph_build.sh +++ b/util/Genome_Biology/metagraph_scripts/metagraph_build.sh @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + source /project/archive-index-data/smehringer/benchmark.variables META_DIR="${WORKDIR}/metagraph_bench" diff --git a/util/Genome_Biology/metagraph_scripts/metagraph_query.sh b/util/Genome_Biology/metagraph_scripts/metagraph_query.sh index 578f1e58..16f2d8b1 100755 --- a/util/Genome_Biology/metagraph_scripts/metagraph_query.sh +++ b/util/Genome_Biology/metagraph_scripts/metagraph_query.sh @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + source /project/archive-index-data/smehringer/benchmark.variables META_DIR="${WORKDIR}/metagraph_bench" diff --git a/util/Genome_Biology/new_metagraph_scripts/0_kmc.sh b/util/Genome_Biology/new_metagraph_scripts/0_kmc.sh index eb678044..67999094 100755 --- a/util/Genome_Biology/new_metagraph_scripts/0_kmc.sh +++ b/util/Genome_Biology/new_metagraph_scripts/0_kmc.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail source /project/archive-index-data/seiler/refseq_metagraph/variables.sh diff --git a/util/Genome_Biology/new_metagraph_scripts/1_build.first.sh b/util/Genome_Biology/new_metagraph_scripts/1_build.first.sh index 97069cf3..4d43ae2e 100755 --- a/util/Genome_Biology/new_metagraph_scripts/1_build.first.sh +++ b/util/Genome_Biology/new_metagraph_scripts/1_build.first.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail source /project/archive-index-data/seiler/refseq_metagraph/variables.sh diff --git a/util/Genome_Biology/new_metagraph_scripts/2_transform.sh b/util/Genome_Biology/new_metagraph_scripts/2_transform.sh index ac749e9a..501a11c6 100755 --- a/util/Genome_Biology/new_metagraph_scripts/2_transform.sh +++ b/util/Genome_Biology/new_metagraph_scripts/2_transform.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail source /project/archive-index-data/seiler/refseq_metagraph/variables.sh diff --git a/util/Genome_Biology/new_metagraph_scripts/3_build.second.sh b/util/Genome_Biology/new_metagraph_scripts/3_build.second.sh index 844a85f0..5d2e86d4 100755 --- a/util/Genome_Biology/new_metagraph_scripts/3_build.second.sh +++ b/util/Genome_Biology/new_metagraph_scripts/3_build.second.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail source /project/archive-index-data/seiler/refseq_metagraph/variables.sh diff --git a/util/Genome_Biology/new_metagraph_scripts/4_annotate.sh b/util/Genome_Biology/new_metagraph_scripts/4_annotate.sh index b55d4a27..2dfb4e23 100755 --- a/util/Genome_Biology/new_metagraph_scripts/4_annotate.sh +++ b/util/Genome_Biology/new_metagraph_scripts/4_annotate.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail source /project/archive-index-data/seiler/refseq_metagraph/variables.sh diff --git a/util/Genome_Biology/new_metagraph_scripts/5_transform_anno.sh b/util/Genome_Biology/new_metagraph_scripts/5_transform_anno.sh index 465329c5..38cbd48e 100755 --- a/util/Genome_Biology/new_metagraph_scripts/5_transform_anno.sh +++ b/util/Genome_Biology/new_metagraph_scripts/5_transform_anno.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail source /project/archive-index-data/seiler/refseq_metagraph/variables.sh diff --git a/util/Genome_Biology/new_metagraph_scripts/6_query.sh b/util/Genome_Biology/new_metagraph_scripts/6_query.sh index 06fb63fa..7be2b0b4 100755 --- a/util/Genome_Biology/new_metagraph_scripts/6_query.sh +++ b/util/Genome_Biology/new_metagraph_scripts/6_query.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail source /project/archive-index-data/seiler/refseq_metagraph/variables.sh diff --git a/util/Genome_Biology/new_metagraph_scripts/all.sh b/util/Genome_Biology/new_metagraph_scripts/all.sh index 44e99cf9..f9144081 100755 --- a/util/Genome_Biology/new_metagraph_scripts/all.sh +++ b/util/Genome_Biology/new_metagraph_scripts/all.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail echo -n "[$(date +"%Y-%m-%d %T")] Running KMC..." diff --git a/util/Genome_Biology/new_metagraph_scripts/kmc.helper.sh b/util/Genome_Biology/new_metagraph_scripts/kmc.helper.sh index 00aae840..7e6c8137 100755 --- a/util/Genome_Biology/new_metagraph_scripts/kmc.helper.sh +++ b/util/Genome_Biology/new_metagraph_scripts/kmc.helper.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail source /project/archive-index-data/seiler/refseq_metagraph/variables.sh diff --git a/util/Genome_Biology/new_metagraph_scripts/variables.sh b/util/Genome_Biology/new_metagraph_scripts/variables.sh index 9b6436ee..918fdb56 100755 --- a/util/Genome_Biology/new_metagraph_scripts/variables.sh +++ b/util/Genome_Biology/new_metagraph_scripts/variables.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -eEuo pipefail DATA_DIR="/project/archive-index-data/data/RefSeqCG_arc_bac/v1/files/" diff --git a/util/Genome_Biology/plots/fig_4_many_user_bins.R b/util/Genome_Biology/plots/fig_4_many_user_bins.R index 07916473..a259042c 100644 --- a/util/Genome_Biology/plots/fig_4_many_user_bins.R +++ b/util/Genome_Biology/plots/fig_4_many_user_bins.R @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + library(ggplot2) library(RColorBrewer) library(here) diff --git a/util/Genome_Biology/plots/fig_4_many_user_bins.tsv.license b/util/Genome_Biology/plots/fig_4_many_user_bins.tsv.license new file mode 100644 index 00000000..70b01de1 --- /dev/null +++ b/util/Genome_Biology/plots/fig_4_many_user_bins.tsv.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: CC-BY-4.0 diff --git a/util/Genome_Biology/plots/fig_5_RefSeq_all_tools.R b/util/Genome_Biology/plots/fig_5_RefSeq_all_tools.R index 8d643430..f3a810fb 100755 --- a/util/Genome_Biology/plots/fig_5_RefSeq_all_tools.R +++ b/util/Genome_Biology/plots/fig_5_RefSeq_all_tools.R @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + library(lubridate) library(here) library(ggplot2) diff --git a/util/Genome_Biology/plots/fig_6_acc.R b/util/Genome_Biology/plots/fig_6_acc.R index f6de6946..b8eb1dee 100755 --- a/util/Genome_Biology/plots/fig_6_acc.R +++ b/util/Genome_Biology/plots/fig_6_acc.R @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + library(lubridate) library(ggplot2) library(ggnewscale) diff --git a/util/Genome_Biology/plots/fig_6_acc.csv.license b/util/Genome_Biology/plots/fig_6_acc.csv.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/Genome_Biology/plots/fig_6_acc.csv.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/Genome_Biology/plots/fig_9_tmax_measurements.R b/util/Genome_Biology/plots/fig_9_tmax_measurements.R index 89ed0228..105e2864 100644 --- a/util/Genome_Biology/plots/fig_9_tmax_measurements.R +++ b/util/Genome_Biology/plots/fig_9_tmax_measurements.R @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + library(ggplot2) library(reshape2) library(here) diff --git a/util/Genome_Biology/raptor_scripts/all.sh b/util/Genome_Biology/raptor_scripts/all.sh index 58e97800..8bf244d2 100755 --- a/util/Genome_Biology/raptor_scripts/all.sh +++ b/util/Genome_Biology/raptor_scripts/all.sh @@ -1,10 +1,8 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause set -Eeuo pipefail diff --git a/util/Genome_Biology/raptor_scripts/eval.py b/util/Genome_Biology/raptor_scripts/eval.py index 3c28534d..82c75fe6 100755 --- a/util/Genome_Biology/raptor_scripts/eval.py +++ b/util/Genome_Biology/raptor_scripts/eval.py @@ -1,11 +1,8 @@ #!/usr/bin/env python3 -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause import numpy as np import pandas as pd diff --git a/util/Genome_Biology/raptor_scripts/raptor.sh b/util/Genome_Biology/raptor_scripts/raptor.sh index ce513ccd..c7d5ca05 100755 --- a/util/Genome_Biology/raptor_scripts/raptor.sh +++ b/util/Genome_Biology/raptor_scripts/raptor.sh @@ -1,10 +1,8 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause set -Eeuo pipefail diff --git a/util/Genome_Biology/refseq_truth/generate_truth_file.sh b/util/Genome_Biology/refseq_truth/generate_truth_file.sh index e295b5a0..fc4fbe3d 100644 --- a/util/Genome_Biology/refseq_truth/generate_truth_file.sh +++ b/util/Genome_Biology/refseq_truth/generate_truth_file.sh @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + # all commands used to generate the truth file # create file to validate diff --git a/util/Genome_Biology/refseq_truth/raptor.header.license b/util/Genome_Biology/refseq_truth/raptor.header.license new file mode 100644 index 00000000..70b01de1 --- /dev/null +++ b/util/Genome_Biology/refseq_truth/raptor.header.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: CC-BY-4.0 diff --git a/util/Genome_Biology/refseq_truth/refseq.sample.ids.license b/util/Genome_Biology/refseq_truth/refseq.sample.ids.license new file mode 100644 index 00000000..70b01de1 --- /dev/null +++ b/util/Genome_Biology/refseq_truth/refseq.sample.ids.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: CC-BY-4.0 diff --git a/util/Genome_Biology/refseq_truth/validate_all_reads.sh b/util/Genome_Biology/refseq_truth/validate_all_reads.sh index 9c961abb..bbf81607 100755 --- a/util/Genome_Biology/refseq_truth/validate_all_reads.sh +++ b/util/Genome_Biology/refseq_truth/validate_all_reads.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail export LC_ALL=C export LANG=C diff --git a/util/Genome_Biology/run_all.sh b/util/Genome_Biology/run_all.sh index 9cac12a1..e5671252 100755 --- a/util/Genome_Biology/run_all.sh +++ b/util/Genome_Biology/run_all.sh @@ -1,5 +1,9 @@ #!/bin/bash +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -eEuo pipefail source /path/to/benchmark.variables diff --git a/util/Genome_Biology/scripts/compare.sh b/util/Genome_Biology/scripts/compare.sh index 19c12e28..ef0ce8b7 100644 --- a/util/Genome_Biology/scripts/compare.sh +++ b/util/Genome_Biology/scripts/compare.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail LANG=C # For sort diff --git a/util/Genome_Biology/scripts/compare_simulated.sh b/util/Genome_Biology/scripts/compare_simulated.sh index 0c107905..f77226d7 100644 --- a/util/Genome_Biology/scripts/compare_simulated.sh +++ b/util/Genome_Biology/scripts/compare_simulated.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail LANG=C # For sort diff --git a/util/Genome_Biology/scripts/pretty_scripts/_create_reads.sh b/util/Genome_Biology/scripts/pretty_scripts/_create_reads.sh index 41f4f027..a68d3ff0 100755 --- a/util/Genome_Biology/scripts/pretty_scripts/_create_reads.sh +++ b/util/Genome_Biology/scripts/pretty_scripts/_create_reads.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail export LC_ALL=C export LANG=C diff --git a/util/Genome_Biology/scripts/pretty_scripts/_validate_on_existing_index.sh b/util/Genome_Biology/scripts/pretty_scripts/_validate_on_existing_index.sh index 3769c676..e9b707e4 100755 --- a/util/Genome_Biology/scripts/pretty_scripts/_validate_on_existing_index.sh +++ b/util/Genome_Biology/scripts/pretty_scripts/_validate_on_existing_index.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail export LC_ALL=C export LANG=C diff --git a/util/Genome_Biology/scripts/pretty_scripts/compare.sh b/util/Genome_Biology/scripts/pretty_scripts/compare.sh index d94ea327..83b1609c 100644 --- a/util/Genome_Biology/scripts/pretty_scripts/compare.sh +++ b/util/Genome_Biology/scripts/pretty_scripts/compare.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail export LC_ALL=C export LANG=C diff --git a/util/Genome_Biology/scripts/pretty_scripts/create_indices.sh b/util/Genome_Biology/scripts/pretty_scripts/create_indices.sh index 68d65bc4..7acff216 100644 --- a/util/Genome_Biology/scripts/pretty_scripts/create_indices.sh +++ b/util/Genome_Biology/scripts/pretty_scripts/create_indices.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail export LC_ALL=C export LANG=C diff --git a/util/Genome_Biology/scripts/pretty_scripts/create_reads.sh b/util/Genome_Biology/scripts/pretty_scripts/create_reads.sh index 764cb17b..ded6d18f 100644 --- a/util/Genome_Biology/scripts/pretty_scripts/create_reads.sh +++ b/util/Genome_Biology/scripts/pretty_scripts/create_reads.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail export LC_ALL=C export LANG=C diff --git a/util/Genome_Biology/scripts/pretty_scripts/validate_on_existing_index.sh b/util/Genome_Biology/scripts/pretty_scripts/validate_on_existing_index.sh index f16f8d38..f920e176 100755 --- a/util/Genome_Biology/scripts/pretty_scripts/validate_on_existing_index.sh +++ b/util/Genome_Biology/scripts/pretty_scripts/validate_on_existing_index.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail export LC_ALL=C export LANG=C diff --git a/util/Genome_Biology/scripts/pretty_scripts/validate_single.sh b/util/Genome_Biology/scripts/pretty_scripts/validate_single.sh index 6cbc091f..8b2e4e8c 100755 --- a/util/Genome_Biology/scripts/pretty_scripts/validate_single.sh +++ b/util/Genome_Biology/scripts/pretty_scripts/validate_single.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail export LC_ALL=C export LANG=C diff --git a/util/Genome_Biology/scripts/validate.sh b/util/Genome_Biology/scripts/validate.sh index c4cf0fec..ee22bf40 100755 --- a/util/Genome_Biology/scripts/validate.sh +++ b/util/Genome_Biology/scripts/validate.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail ## ----------------------------------------------------------------------------- diff --git a/util/Genome_Biology/seqothello_scripts/SeqOthello_build.sh b/util/Genome_Biology/seqothello_scripts/SeqOthello_build.sh index 89cdc03d..1a5e93bd 100755 --- a/util/Genome_Biology/seqothello_scripts/SeqOthello_build.sh +++ b/util/Genome_Biology/seqothello_scripts/SeqOthello_build.sh @@ -1,5 +1,9 @@ #!/bin/bash +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + source /project/archive-index-data/smehringer/benchmark.variables OTH_DIR="${WORKDIR}/SeqOthello_bench" diff --git a/util/Genome_Biology/seqothello_scripts/SeqOthello_prep_me.sh b/util/Genome_Biology/seqothello_scripts/SeqOthello_prep_me.sh index e00b7565..fcb92417 100755 --- a/util/Genome_Biology/seqothello_scripts/SeqOthello_prep_me.sh +++ b/util/Genome_Biology/seqothello_scripts/SeqOthello_prep_me.sh @@ -1,5 +1,9 @@ #!/bin/bash +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + source /project/archive-index-data/smehringer/benchmark.variables OTH_DIR="${WORKDIR}/SeqOthello_bench" diff --git a/util/Genome_Biology/seqothello_scripts/SeqOthello_query.sh b/util/Genome_Biology/seqothello_scripts/SeqOthello_query.sh index 07fa03f3..542d416a 100755 --- a/util/Genome_Biology/seqothello_scripts/SeqOthello_query.sh +++ b/util/Genome_Biology/seqothello_scripts/SeqOthello_query.sh @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + source /project/archive-index-data/smehringer/benchmark.variables OTH_DIR="${WORKDIR}/SeqOthello_bench" diff --git a/util/Genome_Biology/seqothello_scripts/call_jellyfish.sh b/util/Genome_Biology/seqothello_scripts/call_jellyfish.sh index 2b625a8f..c101920d 100755 --- a/util/Genome_Biology/seqothello_scripts/call_jellyfish.sh +++ b/util/Genome_Biology/seqothello_scripts/call_jellyfish.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + set -Eeuo pipefail source /project/archive-index-data/smehringer/benchmark.variables diff --git a/util/Genome_Biology/seqothello_scripts/gen.sh b/util/Genome_Biology/seqothello_scripts/gen.sh index 06da85a1..ec6b20be 100755 --- a/util/Genome_Biology/seqothello_scripts/gen.sh +++ b/util/Genome_Biology/seqothello_scripts/gen.sh @@ -1,5 +1,9 @@ #!/bin/bash +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + TOOLCHAIN_PATH_DEFAULT=`pwd`/build/bin read -e -p "Please enter the folder contains SeqOthello toolchain [default: $TOOLCHAIN_PATH_DEFAULT]: " INPUT TOOLCHAIN_PATH="${INPUT:-$TOOLCHAIN_PATH_DEFAULT}" diff --git a/util/applications/include/Genome_Biology/check_output_file.hpp b/util/applications/include/Genome_Biology/check_output_file.hpp index 52fccfa0..9c29b688 100644 --- a/util/applications/include/Genome_Biology/check_output_file.hpp +++ b/util/applications/include/Genome_Biology/check_output_file.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/util/applications/include/Genome_Biology/parse_user_bin_ids.hpp b/util/applications/include/Genome_Biology/parse_user_bin_ids.hpp index 872e19a0..7ed0b3ef 100644 --- a/util/applications/include/Genome_Biology/parse_user_bin_ids.hpp +++ b/util/applications/include/Genome_Biology/parse_user_bin_ids.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include #include diff --git a/util/applications/src/CMakeLists.txt b/util/applications/src/CMakeLists.txt index dc3b1388..8ffa6d64 100644 --- a/util/applications/src/CMakeLists.txt +++ b/util/applications/src/CMakeLists.txt @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + cmake_minimum_required (VERSION 3.25) project (raptor_utility_common LANGUAGES CXX) diff --git a/util/applications/src/Genome_Biology/CMakeLists.txt b/util/applications/src/Genome_Biology/CMakeLists.txt index 0732f575..9def9114 100644 --- a/util/applications/src/Genome_Biology/CMakeLists.txt +++ b/util/applications/src/Genome_Biology/CMakeLists.txt @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + cmake_minimum_required (VERSION 3.25) if (NOT TARGET fasta_to_fastq) diff --git a/util/applications/src/Genome_Biology/compare_to_truth.cpp b/util/applications/src/Genome_Biology/compare_to_truth.cpp index 35863a15..fd3d811e 100644 --- a/util/applications/src/Genome_Biology/compare_to_truth.cpp +++ b/util/applications/src/Genome_Biology/compare_to_truth.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include #include diff --git a/util/applications/src/Genome_Biology/fasta_to_fastq.cpp b/util/applications/src/Genome_Biology/fasta_to_fastq.cpp index 0e3a25d5..b6053a97 100644 --- a/util/applications/src/Genome_Biology/fasta_to_fastq.cpp +++ b/util/applications/src/Genome_Biology/fasta_to_fastq.cpp @@ -1,3 +1,7 @@ +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause + #include #include diff --git a/util/applications/src/Genome_Biology/normalise_yara_truth_file.cpp b/util/applications/src/Genome_Biology/normalise_yara_truth_file.cpp index 4abddf3c..3fb4621e 100644 --- a/util/applications/src/Genome_Biology/normalise_yara_truth_file.cpp +++ b/util/applications/src/Genome_Biology/normalise_yara_truth_file.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// 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/raptor/blob/master/LICENSE.md -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include #include diff --git a/util/applications/src/hibf_sizes.cpp b/util/applications/src/hibf_sizes.cpp index 2e7eac71..7214b1b4 100644 --- a/util/applications/src/hibf_sizes.cpp +++ b/util/applications/src/hibf_sizes.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/util/applications/src/iScience/CMakeLists.txt b/util/applications/src/iScience/CMakeLists.txt index 2c798099..65563df0 100644 --- a/util/applications/src/iScience/CMakeLists.txt +++ b/util/applications/src/iScience/CMakeLists.txt @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + cmake_minimum_required (VERSION 3.25) if (NOT TARGET generate_reads) diff --git a/util/applications/src/iScience/apply_taxsbp.cpp b/util/applications/src/iScience/apply_taxsbp.cpp index 40e54936..4b23bd33 100644 --- a/util/applications/src/iScience/apply_taxsbp.cpp +++ b/util/applications/src/iScience/apply_taxsbp.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/util/applications/src/iScience/count_minimiser.cpp b/util/applications/src/iScience/count_minimiser.cpp index 1af3fef4..47decd16 100644 --- a/util/applications/src/iScience/count_minimiser.cpp +++ b/util/applications/src/iScience/count_minimiser.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include #include diff --git a/util/applications/src/iScience/generate_reads.cpp b/util/applications/src/iScience/generate_reads.cpp index 8411cd73..d0322840 100644 --- a/util/applications/src/iScience/generate_reads.cpp +++ b/util/applications/src/iScience/generate_reads.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/util/applications/src/iScience/generate_reads_refseq.cpp b/util/applications/src/iScience/generate_reads_refseq.cpp index f5f8c3e4..00746fd2 100644 --- a/util/applications/src/iScience/generate_reads_refseq.cpp +++ b/util/applications/src/iScience/generate_reads_refseq.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/util/applications/src/iScience/ibf_fpr.cpp b/util/applications/src/iScience/ibf_fpr.cpp index 46ac0868..4934cef1 100644 --- a/util/applications/src/iScience/ibf_fpr.cpp +++ b/util/applications/src/iScience/ibf_fpr.cpp @@ -1,3 +1,7 @@ +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause + #include int main() diff --git a/util/applications/src/iScience/split_sequence.cpp b/util/applications/src/iScience/split_sequence.cpp index 29db379c..6bb5da0d 100644 --- a/util/applications/src/iScience/split_sequence.cpp +++ b/util/applications/src/iScience/split_sequence.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include diff --git a/util/applications/src/iScience/threshold_info.cpp b/util/applications/src/iScience/threshold_info.cpp index f4893286..02207a17 100644 --- a/util/applications/src/iScience/threshold_info.cpp +++ b/util/applications/src/iScience/threshold_info.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include #include diff --git a/util/iScience/CMakeLists.txt b/util/iScience/CMakeLists.txt index f6f20c1e..8d19c23a 100644 --- a/util/iScience/CMakeLists.txt +++ b/util/iScience/CMakeLists.txt @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/util/iScience/README.md b/util/iScience/README.md index b5c58266..d529f269 100644 --- a/util/iScience/README.md +++ b/util/iScience/README.md @@ -1,3 +1,9 @@ + + # Raptor Utilities This subfolder contains scripts and documentation related to the experiments run in the paper. diff --git a/util/iScience/bash_scripts/benchmark.sh b/util/iScience/bash_scripts/benchmark.sh index 1aa80005..6c5801c4 100755 --- a/util/iScience/bash_scripts/benchmark.sh +++ b/util/iScience/bash_scripts/benchmark.sh @@ -1,11 +1,8 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause set -e diff --git a/util/iScience/bash_scripts/benchmark_wk.sh b/util/iScience/bash_scripts/benchmark_wk.sh index 0a97d994..d69616d9 100755 --- a/util/iScience/bash_scripts/benchmark_wk.sh +++ b/util/iScience/bash_scripts/benchmark_wk.sh @@ -1,11 +1,8 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause set -e diff --git a/util/iScience/bash_scripts/count_minimisers.sh b/util/iScience/bash_scripts/count_minimisers.sh index 477cb8a7..8259e90e 100755 --- a/util/iScience/bash_scripts/count_minimisers.sh +++ b/util/iScience/bash_scripts/count_minimisers.sh @@ -1,11 +1,8 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause set -e diff --git a/util/iScience/bash_scripts/dream_yara.sh b/util/iScience/bash_scripts/dream_yara.sh index acca2c57..e2aa5e2a 100755 --- a/util/iScience/bash_scripts/dream_yara.sh +++ b/util/iScience/bash_scripts/dream_yara.sh @@ -1,11 +1,8 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause set -e diff --git a/util/iScience/bash_scripts/original_dream_yara.sh b/util/iScience/bash_scripts/original_dream_yara.sh index 84b6609a..3a0f340c 100755 --- a/util/iScience/bash_scripts/original_dream_yara.sh +++ b/util/iScience/bash_scripts/original_dream_yara.sh @@ -1,11 +1,8 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause set -e diff --git a/util/iScience/bash_scripts/run_squeakr.sh b/util/iScience/bash_scripts/run_squeakr.sh index 4c9294bc..b5cc5799 100644 --- a/util/iScience/bash_scripts/run_squeakr.sh +++ b/util/iScience/bash_scripts/run_squeakr.sh @@ -1,11 +1,8 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cutoff=50 cutoffs=(1 3 10 20) diff --git a/util/iScience/bash_scripts/simulate.sh b/util/iScience/bash_scripts/simulate.sh index 61850988..da7881e5 100755 --- a/util/iScience/bash_scripts/simulate.sh +++ b/util/iScience/bash_scripts/simulate.sh @@ -1,11 +1,8 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause set -Eeuo pipefail diff --git a/util/iScience/cmake/raptor_require_dream_yara.cmake b/util/iScience/cmake/raptor_require_dream_yara.cmake index aece9c6c..2f5ff2f4 100644 --- a/util/iScience/cmake/raptor_require_dream_yara.cmake +++ b/util/iScience/cmake/raptor_require_dream_yara.cmake @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause macro (raptor_require_dream_yara) set (dream_yara_args ${SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS}) diff --git a/util/iScience/cmake/raptor_require_mason.cmake b/util/iScience/cmake/raptor_require_mason.cmake index c455fd8b..6ef470fa 100644 --- a/util/iScience/cmake/raptor_require_mason.cmake +++ b/util/iScience/cmake/raptor_require_mason.cmake @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause macro (raptor_require_mason) set (mason_args ${SEQAN3_EXTERNAL_PROJECT_CMAKE_ARGS}) diff --git a/util/iScience/evaluation_scripts/eval_benchmark.py b/util/iScience/evaluation_scripts/eval_benchmark.py index 8476cfe1..c63fd3e1 100644 --- a/util/iScience/evaluation_scripts/eval_benchmark.py +++ b/util/iScience/evaluation_scripts/eval_benchmark.py @@ -1,11 +1,8 @@ #!/usr/bin/env python3 -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause import numpy as np import pandas as pd diff --git a/util/iScience/evaluation_scripts/eval_yara.py b/util/iScience/evaluation_scripts/eval_yara.py index a3324bc3..e0a9caad 100644 --- a/util/iScience/evaluation_scripts/eval_yara.py +++ b/util/iScience/evaluation_scripts/eval_yara.py @@ -1,11 +1,8 @@ #!/usr/bin/env python3 -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause import numpy as np import pandas as pd diff --git a/util/iScience/evaluation_scripts/get_counts.py b/util/iScience/evaluation_scripts/get_counts.py index d3530b7d..2e02e16b 100644 --- a/util/iScience/evaluation_scripts/get_counts.py +++ b/util/iScience/evaluation_scripts/get_counts.py @@ -1,11 +1,8 @@ #!/usr/bin/env python3 -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause import numpy as np import pandas as pd diff --git a/util/iScience/evaluation_scripts/get_frequencies.py b/util/iScience/evaluation_scripts/get_frequencies.py index 0e27fed2..9a7ba1c7 100644 --- a/util/iScience/evaluation_scripts/get_frequencies.py +++ b/util/iScience/evaluation_scripts/get_frequencies.py @@ -1,11 +1,8 @@ #!/usr/bin/env python3 -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause import numpy as np import pandas as pd diff --git a/util/iScience/evaluation_scripts/get_thresholds.py b/util/iScience/evaluation_scripts/get_thresholds.py index e0ea10ad..2262b132 100644 --- a/util/iScience/evaluation_scripts/get_thresholds.py +++ b/util/iScience/evaluation_scripts/get_thresholds.py @@ -1,11 +1,8 @@ #!/usr/bin/env python3 -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause import numpy as np import pandas as pd diff --git a/util/iScience/thresholding/CMakeLists.txt b/util/iScience/thresholding/CMakeLists.txt index 3a4919e7..3f75fe03 100644 --- a/util/iScience/thresholding/CMakeLists.txt +++ b/util/iScience/thresholding/CMakeLists.txt @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/util/iScience/thresholding/README.md b/util/iScience/thresholding/README.md index e2b66187..8a71b691 100644 --- a/util/iScience/thresholding/README.md +++ b/util/iScience/thresholding/README.md @@ -1,3 +1,9 @@ + + # Minimizer thresholds This directory contains code to compute thresholds for minimizer-based searches. diff --git a/util/iScience/thresholding/include/heuristic_threshold.hpp b/util/iScience/thresholding/include/heuristic_threshold.hpp index d16b9555..848416a6 100644 --- a/util/iScience/thresholding/include/heuristic_threshold.hpp +++ b/util/iScience/thresholding/include/heuristic_threshold.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \author Enrico Seiler diff --git a/util/iScience/thresholding/include/lemma_threshold.hpp b/util/iScience/thresholding/include/lemma_threshold.hpp index 95bc5170..a1dd90d1 100644 --- a/util/iScience/thresholding/include/lemma_threshold.hpp +++ b/util/iScience/thresholding/include/lemma_threshold.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \author Enrico Seiler diff --git a/util/iScience/thresholding/include/minimizer.hpp b/util/iScience/thresholding/include/minimizer.hpp index c25d4af3..e1b24a4f 100644 --- a/util/iScience/thresholding/include/minimizer.hpp +++ b/util/iScience/thresholding/include/minimizer.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \author Enrico Seiler diff --git a/util/iScience/thresholding/include/minimizer_model.hpp b/util/iScience/thresholding/include/minimizer_model.hpp index 763fa2c9..55b906af 100644 --- a/util/iScience/thresholding/include/minimizer_model.hpp +++ b/util/iScience/thresholding/include/minimizer_model.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \author Enrico Seiler diff --git a/util/iScience/thresholding/include/strong_types.hpp b/util/iScience/thresholding/include/strong_types.hpp index 560d2f5b..ae3a493b 100644 --- a/util/iScience/thresholding/include/strong_types.hpp +++ b/util/iScience/thresholding/include/strong_types.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \author Enrico Seiler diff --git a/util/iScience/thresholding/script/Rscript/combined.R b/util/iScience/thresholding/script/Rscript/combined.R index 08941821..19bc2c52 100644 --- a/util/iScience/thresholding/script/Rscript/combined.R +++ b/util/iScience/thresholding/script/Rscript/combined.R @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + library(ggplot2) library(reshape2) library(gridExtra) diff --git a/util/iScience/thresholding/script/Rscript/counts.R b/util/iScience/thresholding/script/Rscript/counts.R index ffafcc5f..3c46bd79 100644 --- a/util/iScience/thresholding/script/Rscript/counts.R +++ b/util/iScience/thresholding/script/Rscript/counts.R @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + library(ggplot2) library(reshape2) diff --git a/util/iScience/thresholding/script/Rscript/fscore.R b/util/iScience/thresholding/script/Rscript/fscore.R index 9c745845..2f321bd0 100644 --- a/util/iScience/thresholding/script/Rscript/fscore.R +++ b/util/iScience/thresholding/script/Rscript/fscore.R @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + library(ggplot2) library(reshape2) diff --git a/util/iScience/thresholding/script/Rscript/thresholds.R b/util/iScience/thresholding/script/Rscript/thresholds.R index 97d85b90..205cff1d 100644 --- a/util/iScience/thresholding/script/Rscript/thresholds.R +++ b/util/iScience/thresholding/script/Rscript/thresholds.R @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + library(ggplot2) library(reshape2) diff --git a/util/iScience/thresholding/script/Rscript/tnr.R b/util/iScience/thresholding/script/Rscript/tnr.R index e658ff8b..411854b7 100644 --- a/util/iScience/thresholding/script/Rscript/tnr.R +++ b/util/iScience/thresholding/script/Rscript/tnr.R @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + library(ggplot2) library(reshape2) diff --git a/util/iScience/thresholding/script/Rscript/tpr.R b/util/iScience/thresholding/script/Rscript/tpr.R index eac7ce0d..278ffe90 100644 --- a/util/iScience/thresholding/script/Rscript/tpr.R +++ b/util/iScience/thresholding/script/Rscript/tpr.R @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + library(ggplot2) library(reshape2) diff --git a/util/iScience/thresholding/script/jupyter_notebooks/FNR_vs_tau.ipynb.license b/util/iScience/thresholding/script/jupyter_notebooks/FNR_vs_tau.ipynb.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/jupyter_notebooks/FNR_vs_tau.ipynb.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/jupyter_notebooks/FPR_vs_tau.ipynb.license b/util/iScience/thresholding/script/jupyter_notebooks/FPR_vs_tau.ipynb.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/jupyter_notebooks/FPR_vs_tau.ipynb.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/jupyter_notebooks/FScore_vs_tau.ipynb.license b/util/iScience/thresholding/script/jupyter_notebooks/FScore_vs_tau.ipynb.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/jupyter_notebooks/FScore_vs_tau.ipynb.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/jupyter_notebooks/ROC.ipynb.license b/util/iScience/thresholding/script/jupyter_notebooks/ROC.ipynb.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/jupyter_notebooks/ROC.ipynb.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/jupyter_notebooks/TNR_vs_tau.ipynb.license b/util/iScience/thresholding/script/jupyter_notebooks/TNR_vs_tau.ipynb.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/jupyter_notebooks/TNR_vs_tau.ipynb.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/jupyter_notebooks/TPR_vs_tau.ipynb.license b/util/iScience/thresholding/script/jupyter_notebooks/TPR_vs_tau.ipynb.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/jupyter_notebooks/TPR_vs_tau.ipynb.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/jupyter_notebooks/numMin_vs_threshold.ipynb.license b/util/iScience/thresholding/script/jupyter_notebooks/numMin_vs_threshold.ipynb.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/jupyter_notebooks/numMin_vs_threshold.ipynb.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/jupyter_notebooks/tables.ipynb.license b/util/iScience/thresholding/script/jupyter_notebooks/tables.ipynb.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/jupyter_notebooks/tables.ipynb.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/jupyter_notebooks/tables_timing.ipynb.license b/util/iScience/thresholding/script/jupyter_notebooks/tables_timing.ipynb.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/jupyter_notebooks/tables_timing.ipynb.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/run.sh b/util/iScience/thresholding/script/run.sh index 3a5d3523..fd2a3f20 100644 --- a/util/iScience/thresholding/script/run.sh +++ b/util/iScience/thresholding/script/run.sh @@ -1,5 +1,9 @@ #!/usr/bin/env bash +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + # Exit on error set -e diff --git a/util/iScience/thresholding/script/svg_plots/complete.svg.license b/util/iScience/thresholding/script/svg_plots/complete.svg.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/svg_plots/complete.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/svg_plots/f_100.svg.license b/util/iScience/thresholding/script/svg_plots/f_100.svg.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/svg_plots/f_100.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/svg_plots/f_150.svg.license b/util/iScience/thresholding/script/svg_plots/f_150.svg.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/svg_plots/f_150.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/svg_plots/f_250.svg.license b/util/iScience/thresholding/script/svg_plots/f_250.svg.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/svg_plots/f_250.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/svg_plots/mini_100.svg.license b/util/iScience/thresholding/script/svg_plots/mini_100.svg.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/svg_plots/mini_100.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/svg_plots/mini_150.svg.license b/util/iScience/thresholding/script/svg_plots/mini_150.svg.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/svg_plots/mini_150.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/svg_plots/mini_250.svg.license b/util/iScience/thresholding/script/svg_plots/mini_250.svg.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/svg_plots/mini_250.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/svg_plots/tnr_100.svg.license b/util/iScience/thresholding/script/svg_plots/tnr_100.svg.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/svg_plots/tnr_100.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/svg_plots/tnr_150.svg.license b/util/iScience/thresholding/script/svg_plots/tnr_150.svg.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/svg_plots/tnr_150.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/svg_plots/tnr_250.svg.license b/util/iScience/thresholding/script/svg_plots/tnr_250.svg.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/svg_plots/tnr_250.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/svg_plots/tpr_100.svg.license b/util/iScience/thresholding/script/svg_plots/tpr_100.svg.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/svg_plots/tpr_100.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/svg_plots/tpr_150.svg.license b/util/iScience/thresholding/script/svg_plots/tpr_150.svg.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/svg_plots/tpr_150.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/script/svg_plots/tpr_250.svg.license b/util/iScience/thresholding/script/svg_plots/tpr_250.svg.license new file mode 100644 index 00000000..706402f5 --- /dev/null +++ b/util/iScience/thresholding/script/svg_plots/tpr_250.svg.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: BSD-3-Clause diff --git a/util/iScience/thresholding/src/query.cpp b/util/iScience/thresholding/src/query.cpp index 2803b0a3..548b9f20 100644 --- a/util/iScience/thresholding/src/query.cpp +++ b/util/iScience/thresholding/src/query.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \author Enrico Seiler diff --git a/util/iScience/thresholding/src/random_data.cpp b/util/iScience/thresholding/src/random_data.cpp index 91dc317a..5af2a30a 100644 --- a/util/iScience/thresholding/src/random_data.cpp +++ b/util/iScience/thresholding/src/random_data.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// 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/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause /*!\file * \author Enrico Seiler diff --git a/util/new/README.md b/util/new/README.md index 680388a0..f9a7d252 100644 --- a/util/new/README.md +++ b/util/new/README.md @@ -1 +1,7 @@ + + Work in progress for new benchmark scripts diff --git a/util/new/run.sh b/util/new/run.sh index 594cd96d..e76b3c62 100755 --- a/util/new/run.sh +++ b/util/new/run.sh @@ -1,11 +1,8 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause set -Eeuo pipefail diff --git a/util/new/simulate.sh b/util/new/simulate.sh index c9ef7396..d24e6f95 100644 --- a/util/new/simulate.sh +++ b/util/new/simulate.sh @@ -1,11 +1,8 @@ #!/usr/bin/env bash -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause set -Eeuo pipefail diff --git a/util/test/CMakeLists.txt b/util/test/CMakeLists.txt index 61013d73..2d67ce01 100644 --- a/util/test/CMakeLists.txt +++ b/util/test/CMakeLists.txt @@ -1,9 +1,6 @@ -# -------------------------------------------------------------------------------------------------- -# 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/raptor/blob/main/LICENSE.md -# -------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause cmake_minimum_required (VERSION 3.25) diff --git a/workflow/cwl/raptor-build.cwl b/workflow/cwl/raptor-build.cwl index 77c5acdb..625de90e 100644 --- a/workflow/cwl/raptor-build.cwl +++ b/workflow/cwl/raptor-build.cwl @@ -1,4 +1,7 @@ #!/usr/bin/env cwl-runner +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 cwlVersion: v1.2 class: CommandLineTool @@ -86,6 +89,6 @@ arguments: outputs: index: - type: File + type: File outputBinding: glob: $(inputs.output_name) diff --git a/workflow/cwl/raptor-search.cwl b/workflow/cwl/raptor-search.cwl index 3102ad04..8c67c476 100644 --- a/workflow/cwl/raptor-search.cwl +++ b/workflow/cwl/raptor-search.cwl @@ -1,4 +1,7 @@ #!/usr/bin/env cwl-runner +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 cwlVersion: v1.2 class: CommandLineTool @@ -66,7 +69,7 @@ outputs: results: type: File label: Search results - doc: | + doc: | Format: query id + tab + comma separated list of bin numbers that contain matches outputBinding: glob: $(inputs.output_name) diff --git a/workflow/cwl/tests/raptor-build-0_bins_window_19.yml b/workflow/cwl/tests/raptor-build-0_bins_window_19.yml index 3aeae4f6..77ca5b65 100644 --- a/workflow/cwl/tests/raptor-build-0_bins_window_19.yml +++ b/workflow/cwl/tests/raptor-build-0_bins_window_19.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + index_size: 64k kmer_size: 19 window_size: 19 diff --git a/workflow/cwl/tests/raptor-build-16_bins_window_19.yml b/workflow/cwl/tests/raptor-build-16_bins_window_19.yml index 322b9937..818728ff 100644 --- a/workflow/cwl/tests/raptor-build-16_bins_window_19.yml +++ b/workflow/cwl/tests/raptor-build-16_bins_window_19.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + index_size: 64k kmer_size: 19 window_size: 19 diff --git a/workflow/cwl/tests/raptor-search-0_bins_19_window_0_errors.yml b/workflow/cwl/tests/raptor-search-0_bins_19_window_0_errors.yml index 58d76fa9..e4e02350 100644 --- a/workflow/cwl/tests/raptor-search-0_bins_19_window_0_errors.yml +++ b/workflow/cwl/tests/raptor-search-0_bins_19_window_0_errors.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + index: class: File path: ../../../test/data/1bins19window.index diff --git a/workflow/galaxy/.shed.yml b/workflow/galaxy/.shed.yml index d25fb206..13b125c6 100644 --- a/workflow/galaxy/.shed.yml +++ b/workflow/galaxy/.shed.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + categories: - Sequence Analysis description: 'Raptor: pre-filter for querying very large collection' diff --git a/workflow/galaxy/README.md b/workflow/galaxy/README.md index 841674a8..a4284a87 100644 --- a/workflow/galaxy/README.md +++ b/workflow/galaxy/README.md @@ -1,3 +1,9 @@ + + # raptor-galaxy This readme explains how to add a tool to bioconda and galaxy (by using planemo). diff --git a/workflow/galaxy/raptor-build.xml b/workflow/galaxy/raptor-build.xml index 401d50b5..cb0c54cb 100644 --- a/workflow/galaxy/raptor-build.xml +++ b/workflow/galaxy/raptor-build.xml @@ -1,3 +1,9 @@ + + Builds an index to be used by `raptor search`. diff --git a/workflow/galaxy/raptor-search.xml b/workflow/galaxy/raptor-search.xml index 4ecb9765..6a6f0158 100644 --- a/workflow/galaxy/raptor-search.xml +++ b/workflow/galaxy/raptor-search.xml @@ -1,3 +1,9 @@ + + Queries an index to determine which fasta file the query can be found in. diff --git a/workflow/nextflow/README.md b/workflow/nextflow/README.md index 910c40a7..e7811493 100644 --- a/workflow/nextflow/README.md +++ b/workflow/nextflow/README.md @@ -1,3 +1,9 @@ + + # HIBF in Nextflow If you want to include the HIBF in Nextflow, you can adapt this sample workflow `hibf.nf`. diff --git a/workflow/nextflow/hibf.nf b/workflow/nextflow/hibf.nf index 40242bd6..a762af5f 100644 --- a/workflow/nextflow/hibf.nf +++ b/workflow/nextflow/hibf.nf @@ -1,4 +1,8 @@ #!/usr/bin/env nextflow +/* SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin + * SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik + * SPDX-License-Identifier: CC0-1.0 + */ nextflow.enable.dsl=2 /*