VERSIONINFO.md

v0.3.5 - 04.11.2026

• Fixed complement table bug: lowercase 'c' was incorrectly complemented to 't' instead of 'g'
• Fixed off-by-one in tile overlap detection that caused adjacent non-overlapping tiles to be incorrectly skipped during probe selection, reducing yield
• Removed duplicate __len__ method in Tile class (shadowed definition had off-by-one)

v0.3.4 - 04.10.2026

• Fixed designProbes/designProbesBatch reading the species registry from the package install directory instead of ~/.hcrprobedesign/HCRconfig.yaml, which caused "Registered species: none" errors after pip install -U even when listReferences showed registered references

v0.3.3 - 04.08.2026

• Added --large-index flag to buildGenomeIndex for genomes > 4 billion bases

v0.3.2 - 04.08.2026

• Fixed migration bug where species config entries were not restored after pip install -U
• Index directories found in the old package location are now auto-registered as species

v0.3.1 - 04.08.2026

• Moved config and indices to persistent user data directory (~/.hcrprobedesign/)
• Reference genomes and configuration now survive pip install -U upgrades
• Automatic migration of data from old package-relative locations
• Support HCRPROBEDESIGN_DATA_DIR environment variable to override data location

v0.3.0 - 04.08.2026

• Added listReferences CLI tool to display installed reference genomes and default parameters
• Added HCRProbeDesign.listReferences module with programmatic access to reference info
• Documentation base URL updated

v0.2.4 - 01.16.2026

• Exposed package version in HCRProbeDesign.__version__

v0.2.3 - 01.14.2026

• Added detailed documentation
• Added loader for custom reference genomes
• Added batch-processing of multi-record fasta files

v0.2.2 - 1.7.2022

• Added --idt argument to format output probes for IDT ordering on plates

v0.2.1 - 5.10.2021

• Merged packaging branch into master
• HCRProbeDesign is now packaged as a pip-installable Utility
• Added designProbes as entry point for cmdline access
• Added fetchIndex as entry point to grab and install (default mm10) bowtie2 index
• Updated dependencies to include zipfile36