kemalandClaude Opus 5.5
9149ef328a
* simurg/core/brand.py: single source of the mark geometry, colours, favicon and the report header band (scripts/brand now load it from there). * HTML reports (QC report, compare dashboard, methylation QC): offline SVG favicon, indigo header band with the mark, version and a sha256 of the data shown; Noto Sans font stack; methylation plots in Okabe-Ito colours. * README banner, guide logo, brand/blog links; branding brief updated to the final identity; Noto (OFL) and Okabe-Ito entries in THIRD_PARTY_NOTICES; CHANGELOG (Unreleased). Unit tests + P5 QC oracle: 285 passed; ruff and mypy clean. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
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# 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 (gzip-compressed) in `simurg/qc/report/vendor/plotly.min.js.gz` 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) — Copyright Illumina, Inc. | Apache-2.0 | Indel source-sequence handling ported to `simurg/harmonize/sites.py` (design-strand orientation, left shift, IUPAC flank matching, deletion/insertion context score); multi-probe consistency idea in `simurg/harmonize/combine.py`; test oracle (run under Python 3 with two local compatibility patches, never shipped) |
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| [Picard `picard.arrays`](https://github.com/broadinstitute/picard) | MIT | Second format reference |
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| [PyO3](https://github.com/PyO3/pyo3), [rust-numpy](https://github.com/PyO3/rust-numpy), [ndarray](https://github.com/rust-ndarray/ndarray) and their Rust dependencies | MIT / Apache-2.0 / BSD-2-Clause | Compiled into the optional `simurg_core` extension (`rust/simurg-core`); list with `cargo tree` |
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| [UCSC Genome Browser](https://genome.ucsc.edu/) `cytoBand` tables (hg38, hg19) and `ncbiRefSeq` (RefSeq transcripts, NCBI) | Free for all uses (UCSC data terms; RefSeq is public domain) | `simurg/cn/data/cytoBand_GRCh3{7,8}.txt.gz` and the derived centromere/acrocentric mask BEDs are shipped; `scripts/build_annotation_bundle.sh` downloads cytoBand + ncbiRefSeq for gene lists; `simurg/pgx/data/pgx_cn_regions.GRCh38.v1.bed` is derived from ncbiRefSeq exon coordinates (`scripts/pgx/build_cn_regions.py`) |
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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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| [CPIC](https://cpicpgx.org) database via the CPIC API (allele definitions, allele function, diplotype→phenotype tables) | CC0 1.0 | downloaded by `scripts/pgx/fetch_sources.sh` into `data/` (never committed); `simurg pgx db build` derives the local PGx DB from it; source version and file hashes are recorded in the DB `meta` table |
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| [PharmVar](https://www.pharmvar.org) haplotype definitions (Gaedigk et al. 2018 CPT 103:399) | PharmVar terms of use (attribution) | per-gene zips downloaded by `scripts/pgx/fetch_sources.sh` into `data/` (never committed); `simurg pgx db build` derives core-allele definitions for genes CPIC does not define |
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| [GeT-RM](https://www.cdc.gov/lab-quality/php/get-rm/reference-materials.html) consolidated PGx/HLA table (CDC) | US government work | validation truth only (`scripts/pgx/getrm_truth.py`), not redistributed |
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| [ClinPGx](https://www.clinpgx.org) (formerly PharmGKB) clinical-annotation variants | CC BY-SA 4.0 (attribution: ClinPGx, https://www.clinpgx.org/page/citingClinpgx) | `clinicalVariants.zip` downloaded by `scripts/pgx/fetch_sources.sh` into `data/` (never committed); rsIDs become genotype-only variant-based genes in the local PGx DB |
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| [Noto Sans, Noto Sans Mono](https://fonts.google.com/noto) — Copyright 2022 The Noto Project Authors | SIL Open Font License 1.1 | Glyph outlines of the wordmark in `branding/logo/` (converted to SVG paths by `scripts/brand/make_brand.py`); named in report CSS but never bundled |
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| Okabe and Ito colour-universal-design palette (Okabe & Ito 2008, *Color Universal Design*) | free to use (cited) | Chart colours in `simurg/core/brand.py` and the HTML reports |
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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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## Apache-2.0 (GTCtoVCF, verbatim LICENSE)
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```
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Apache License
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http://www.apache.org/licenses/
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