kemalandClaude Opus 5.5
95be85a76b
- pipeline/qc_report: dataset discovery/labels/types (QC-041..043), robust TSV/CSV reading (QC-061), join + unmatched warning (QC-040), privacy options (QC-046), xlsx (4 sheets, conditional fills) / csv table (QC-045), byte-deterministic HTML with gzip+base64 embedded data (QC-044, QC-047) - qc/report: template, CSS and JS app — Control Dashboard, Automated QC (table with sort/filter/search/ paging/column menu/export, metric scatters with threshold lines), Sample Heatmaps (chip/plate, continuous/binary), Trend Analysis (grouped summary, Tukey box plots, counts, sex, PCA), thresholds modal (apply / download / upload YAML), linked selection across plots and table (QC-048..060) - bundled plotly.js 2.35.2 (MIT); openpyxl dependency (MIT) - tests: discovery/labels/errors/determinism/xlsx + headless-browser self-test - known_unknowns K-020: remaining report deviations Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
101 lines
5.6 KiB
Markdown
101 lines
5.6 KiB
Markdown
# Third-party notices
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SimurgArray is MIT-licensed. It uses the following sources under their licences (plan §2). GPL-licensed tools are
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used only as external subprocess oracles and are not copied or linked.
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| Source | Licence | How it is used |
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| [Illumina BeadArrayFiles](https://github.com/Illumina/BeadArrayFiles) — Copyright (c) 2020, Illumina | BSD-2-Clause | File-format layouts (GTC, BPM, EGT), normalization-bin rule, `GTC_File_Format_v5.pdf`; locus-summary formulas (`examples/locus_summary.py`, ported to `simurg/qc/locus_summary.py`); test oracle |
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| [gtc2vcf / idat2gtc](https://github.com/freeseek/gtc2vcf) — Copyright (C) 2018-2025 Giulio Genovese | MIT | IDAT field codes, BPM locus-entry order, EGT data-block variants, GTC write order, assay-type inference (`infer_assay_type`); BAF-regression numerics (`BAFregress.c`, `simurg/qc/contamination.py`); test oracle |
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| [plotly.js](https://github.com/plotly/plotly.js) 2.35.2 — Copyright (c) 2021 Plotly, Inc | MIT | Bundled verbatim in `simurg/qc/report/vendor/plotly.min.js` and inlined into QC reports (licence files alongside) |
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| [openpyxl](https://foss.heptapod.net/openpyxl/openpyxl) | MIT | Runtime dependency: `.xlsx` QC table (not vendored) |
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| [klib `ksort.h`](https://github.com/attractivechaos/klib) as shipped in htslib — Copyright (c) 2008, 2012-2013, 2017-2019 Genome Research Ltd | MIT | Quickselect `ks_ksmall` partition order, ported to `simurg/qc/contamination.py` (`ks_ksmall`) to reproduce BAFregress medians |
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| [Illumina GTCtoVCF](https://github.com/Illumina/GTCtoVCF) | Apache-2.0 | VCF conversion rules (phase P6) |
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| [Picard `picard.arrays`](https://github.com/broadinstitute/picard) | MIT | Second format reference |
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| [illuminaio](https://github.com/HenrikBengtsson/illuminaio) | GPL-2 | Documentation of IDAT field codes only; oracle via subprocess |
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## BSD-2-Clause (BeadArrayFiles, verbatim from its README)
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```
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Copyright (c) 2020, Illumina
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
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ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
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(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
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ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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The views and conclusions contained in the software and documentation are those
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of the authors and should not be interpreted as representing official policies,
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either expressed or implied, of the FreeBSD Project.
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```
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## MIT (gtc2vcf, verbatim LICENSE)
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```
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The MIT License
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Copyright (C) 2018-2025 Giulio Genovese
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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THE SOFTWARE.
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```
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## MIT (klib `ksort.h` in htslib, licence header verbatim)
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```
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The MIT License
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Copyright (c) 2008, 2012-2013, 2017-2019 Genome Research Ltd (GRL).
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
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BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
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ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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```
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