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26 changes: 25 additions & 1 deletion CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,29 @@ All notable changes to ModDotPlot Browser are recorded here. The project follows

## [Unreleased]

## [1.0.3] - 2026-10-12

### Added

* Added intersecting imported annotation names to the main plot hover card, grouped
beneath their corresponding X or Y genomic coordinates.
* Added selected GC% and CpG O/E values to the main plot hover card for both axes.

### Changed

* Large landing-page annotations are parsed initially for only the chromosomes in
the active plot and retained for on-demand parsing when other chromosomes are
selected, reducing startup work for whole-genome GFF/GTF files.
* Reorganized plot hover details into distinct X and Y sections for faster reading.
* Simplified citation metadata and consolidated the palette license notices.

### Fixed

* Removed crosshair lag over dense imported annotations by caching the base feature
canvas and painting coalesced hover highlights on a separate overlay.
* Enforced the one-million-feature annotation limit cumulatively across deferred
chromosome batches from the same file.

## [1.0.2] - 2026-10-11

### Changed
Expand Down Expand Up @@ -788,7 +811,8 @@ All notable changes to ModDotPlot Browser are recorded here. The project follows
* Session persistence and data/image export are not implemented.
* Browser compatibility and graphics recovery need broader automated coverage.

[Unreleased]: https://github.com/marbl/ModDotPlot-Browser/compare/v1.0.2...HEAD
[Unreleased]: https://github.com/marbl/ModDotPlot-Browser/compare/v1.0.3...HEAD
[1.0.3]: https://github.com/marbl/ModDotPlot-Browser/compare/v1.0.2...v1.0.3
[1.0.2]: https://github.com/marbl/ModDotPlot-Browser/compare/v1.0.1...v1.0.2
[1.0.1]: https://github.com/marbl/ModDotPlot-Browser/compare/v1.0.0...v1.0.1
[0.9.8]: https://github.com/marbl/ModDotPlot-Browser/compare/v0.9.7...v0.9.8
Expand Down
206 changes: 3 additions & 203 deletions CITATION.cff
Original file line number Diff line number Diff line change
@@ -1,16 +1,11 @@
cff-version: 1.2.0
message: >-
If you use ModDotPlot Browser, please cite the original ModDotPlot paper listed as the
preferred citation and credit the relevant method papers listed in references.
message: "If you use ModDotPlot Browser, please cite the original ModDotPlot paper."
title: "ModDotPlot Browser"
type: software
version: 1.0.2
date-released: 2026-10-11
version: 1.0.3
date-released: 2026-10-12
repository-code: "https://github.com/marbl/ModDotPlot-Browser"
license: MIT-0
abstract: >-
Browser-native genomic dotplot software written by ChatGPT 5.6 Sol under the
direction of Adam Phillippy.
authors:
- name: "ChatGPT 5.6 Sol"
- family-names: "Phillippy"
Expand All @@ -26,200 +21,5 @@ preferred-citation:
given-names: "Michael C."
- family-names: "Phillippy"
given-names: "Adam M."
journal: "Bioinformatics"
year: 2024
month: 8
volume: 40
issue: 8
pages: "btae493"
doi: "10.1093/bioinformatics/btae493"
url: "https://pubmed.ncbi.nlm.nih.gov/39110522/"
notes: "PMID: 39110522; PMCID: PMC11321072."

references:
- type: article
title: "Mash: fast genome and metagenome distance estimation using MinHash"
authors:
- family-names: "Ondov"
given-names: "Brian D."
- family-names: "Treangen"
given-names: "Todd J."
- family-names: "Melsted"
given-names: "Páll"
- family-names: "Mallonee"
given-names: "Adam B."
- family-names: "Bergman"
given-names: "Nicholas H."
- family-names: "Koren"
given-names: "Sergey"
- family-names: "Phillippy"
given-names: "Adam M."
journal: "Genome Biology"
year: 2016
volume: 17
issue: 1
pages: "132"
doi: "10.1186/s13059-016-0997-x"
url: "https://pubmed.ncbi.nlm.nih.gov/27323842/"

- type: article
title: "A fast approximate algorithm for mapping long reads to large reference databases"
authors:
- family-names: "Jain"
given-names: "Chirag"
- family-names: "Dilthey"
given-names: "Alexander"
- family-names: "Koren"
given-names: "Sergey"
- family-names: "Aluru"
given-names: "Srinivas"
- family-names: "Phillippy"
given-names: "Adam M."
journal: "Journal of Computational Biology"
year: 2018
volume: 25
issue: 7
pages: "766-779"
doi: "10.1089/cmb.2018.0036"
url: "https://pubmed.ncbi.nlm.nih.gov/29708767/"

- type: article
title: "Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation"
authors:
- family-names: "Kille"
given-names: "Bryce"
- family-names: "Garrison"
given-names: "Erik"
- family-names: "Treangen"
given-names: "Todd J."
- family-names: "Phillippy"
given-names: "Adam M."
journal: "Bioinformatics"
year: 2023
volume: 39
issue: 9
pages: "btad512"
doi: "10.1093/bioinformatics/btad512"
url: "https://academic.oup.com/bioinformatics/article/39/9/btad512/7246743"

- type: article
title: "ntHash2: recursive spaced seed hashing for nucleotide sequences"
authors:
- family-names: "Kazemi"
given-names: "Parham"
- family-names: "Wong"
given-names: "Johnathan"
- family-names: "Nikolić"
given-names: "Vladimir"
- family-names: "Mohamadi"
given-names: "Hamid"
- family-names: "Warren"
given-names: "René L."
- family-names: "Birol"
given-names: "Inanç"
journal: "Bioinformatics"
year: 2022
volume: 38
issue: 20
pages: "4812-4813"
doi: "10.1093/bioinformatics/btac564"
url: "https://academic.oup.com/bioinformatics/article/38/20/4812/6674501"

- type: conference-paper
title: "b-Bit minwise hashing"
authors:
- family-names: "Li"
given-names: "Ping"
- family-names: "König"
given-names: "Arnd Christian"
collection-title: "Proceedings of the 19th International Conference on World Wide Web"
year: 2010
pages: "671-680"
doi: "10.1145/1772690.1772759"
url: "https://doi.org/10.1145/1772690.1772759"

- type: conference-paper
title: "One permutation hashing"
authors:
- family-names: "Li"
given-names: "Ping"
- family-names: "Owen"
given-names: "Art B."
- family-names: "Zhang"
given-names: "Cun-Hui"
collection-title: "Advances in Neural Information Processing Systems 25"
year: 2012
pages: "3122-3130"
url: "https://papers.nips.cc/paper_files/paper/2012/hash/eaa32c96f620053cf442ad32258076b9-Abstract.html"

- type: conference-paper
title: "HyperLogLog: the analysis of a near-optimal cardinality estimation algorithm"
authors:
- family-names: "Flajolet"
given-names: "Philippe"
- family-names: "Fusy"
given-names: "Éric"
- family-names: "Gandouet"
given-names: "Olivier"
- family-names: "Meunier"
given-names: "Frédéric"
collection-title: "Discrete Mathematics and Theoretical Computer Science Proceedings, Analysis of Algorithms 2007"
year: 2007
volume: "AH"
pages: "127-146"
url: "https://algo.inria.fr/flajolet/Publications/FlFuGaMe07.pdf"

- type: conference-paper
title: "On the resemblance and containment of documents"
authors:
- family-names: "Broder"
given-names: "Andrei Z."
collection-title: "Compression and Complexity of Sequences 1997"
year: 1997
pages: "21-29"
doi: "10.1109/SEQUEN.1997.666900"
url: "https://doi.org/10.1109/SEQUEN.1997.666900"

- type: software
title: "ModDotPlot"
authors:
- family-names: "Sweeten"
given-names: "Alexander P."
- family-names: "Schatz"
given-names: "Michael C."
- family-names: "Phillippy"
given-names: "Adam M."
repository-code: "https://github.com/marbl/moddotplot"

- type: software
title: "MashMap"
authors:
- name: "MashMap contributors"
repository-code: "https://github.com/marbl/MashMap"
commit: "1a07d0e"

- type: software
title: "ntHash"
authors:
- name: "BCGSC ntHash contributors"
repository-code: "https://github.com/bcgsc/ntHash"
commit: "c26bd4572a19de81e30d55042dbd33c1fd21d4b6"

- type: software
title: "SMHasher and the MurmurHash3 reference implementation"
authors:
- family-names: "Appleby"
given-names: "Austin"
url: "https://github.com/aappleby/smhasher/blob/master/src/MurmurHash3.cpp"

- type: software
title: "ColorBrewer 2"
version: "2.0"
authors:
- family-names: "Brewer"
given-names: "Cynthia"
- family-names: "Harrower"
given-names: "Mark"
- name: "The Pennsylvania State University"
repository-code: "https://github.com/axismaps/colorbrewer"
url: "https://colorbrewer2.org/"
92 changes: 0 additions & 92 deletions CONTRIBUTING.md

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4 changes: 2 additions & 2 deletions Cargo.lock

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion Cargo.toml
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ members = ["crates/core", "crates/wasm"]
resolver = "2"

[workspace.package]
version = "1.0.2"
version = "1.0.3"
edition = "2024"
license = "MIT-0"
repository = "https://github.com/marbl/ModDotPlot-Browser"
Expand Down
13 changes: 0 additions & 13 deletions D3_SCALE_CHROMATIC_LICENSE.txt

This file was deleted.

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