v1.1.1

[1.1.1] - 2026-04-29

Added

• --trix / --no-trix: Explicitly enable/disable Trix index generation. Enabled by default when ixIxx is available.
• Adding docker, singularity and conda support

Fixed

• Chrom sizes for validation tracks: chrom.sizes generation now considers validation inputs (e.g. STAR SJ) to avoid bedToBigBed failures when validation coordinates exceed transcript extents.
• Trix generation compatibility: Removed unsupported ixIxx argument usage so Trix generation works with standard UCSC binaries.

v1.1.0

[1.1.0] - 2025-02-16

Added

• --category-tracks: Create tracks only for specified structural categories. Comma-separated abbreviated names (FSM, ISM, NIC, NNC, antisense, genic_intron, genic_genomic, intergenic, fusion). Example: --category-tracks FSM,ISM,NIC
• --hub-name: Optional display name for the hub and prefix for all track labels. Use when loading multiple hubs (e.g. SQANTI-reads samples) so tracks appear as "Name SQANTI3 Transcripts", "Name full-splice_match", etc., making comparison in the UCSC Genome Browser easier.
• Packaging: pyproject.toml for modern Python packaging
• CLI entry point: sqanti_browser command (after pip install -e .)
• Modular architecture: Split core logic into BedProcessor, HubGenerator, ValidationTrackBuilder
• Type hints: Added to public APIs across the codebase
• Unit tests: tests/test_unit.py for utilities, color parsing, constants
• Edge case tests: tests/test_edge_cases.py for missing files, empty inputs, CLI handling
• Constants module: Centralized filter limits (e.g. exon count ≤400, transcript length ≤150 kb) in src/constants.py
• Documentation: "How to run" clarification (python -m sqanti_browser vs sqanti_browser vs python sqanti_browser.py)

Changed

• Renamed: sqanti3_to_UCSC.py → sqanti_browser.py (git history preserved)
• Recommended run command: Use python -m sqanti_browser so the active Python (e.g. conda) is always used
• Project layout: src/, tests/, example/ directories; filter_isoforms.py moved to src/
• CI: GitHub Actions updated with pip install -e ., PYTHONPATH, unit and edge tests
• Filter limits: Increased max exon count (200→400) and transcript length (100 kb→150 kb) for biologically realistic genes (TTN, DMD)

Fixed

• CI cwd and PYTHONPATH for reliable test execution
• Import paths after module reorganization

v1.0.0

Finalized version 1 including expression sorting and coloring.

v0.9.1-beta0

Included functionality for CAGE peaks, polyA, reference Genome, and included examples on wiki about how to check hub formats with genePredCheck, as well as how to work with the output of SQANTI-reads

v0.9.0-beta0

First release of SQANTI-browser for beta-testing.