v0.10.1

What's New in v0.10.1

Features

• Add hivtrace_version field to JSON output for version tracking
• Version is dynamically read from package metadata for single source of truth

Technical Details

• Uses importlib.metadata to read version from setup.py
• Enables future compatibility checking for features like true-append
• Fallback version handling for development mode

Full Changelog: v0.10.0...v0.10.1

Release v0.10.0

Release v0.10.0

This release migrates HIV-TRACE from BioExt/bealign to cawlign for sequence alignment, simplifying the alignment workflow and removing the BioExt dependency.

Major Changes

Alignment Migration

• Replaced BioExt/bealign + bam2msa two-step workflow with single cawlign call
• Removed BAM intermediate file format - cawlign outputs FASTA directly
• Simplified phase tracking by removing BAM_FASTA_CONVERSION phase

New CLI Options

• --cawlign: Path to cawlign executable (defaults to 'cawlign' in PATH)
• --score-matrix: Score matrix for alignment (defaults to 'HIV_BETWEEN_F')

Dependency Changes

• Removed: bioext >= 0.21.8 (no longer required)
• Added: cawlign v1.0.3+ (non-PyPI dependency)

Other Improvements

• Added validate_cawlign() function to warn if cawlign is not found
• Improved error handling for alignment failures
• Updated documentation for cawlign usage

Technical Details

The cawlign command uses:

• -s SCORE_MATRIX: Alignment scoring matrix
• -t codon: Codon-aware alignment mode (required for HIV_BETWEEN_F)
• -I: Include reference sequence in output
• -r reference: Specify reference sequence file

Requirements

• Python >= 3.10
• cawlign v1.0.3+ (install separately)
• tn93 (install separately)

Testing

All 14 existing tests pass with the new implementation.

Installation

pip install hivtrace==0.10.0

Note: You must install cawlign v1.0.3+ separately. See cawlign repository for installation instructions.

0.9.2

Changes

• Renamed "HIV-TRACE True Append" to "TN93 True Append"
• Manually flush output file after each step of tn93 True Append
• Fixed true append pipeline issues
• Various improvements and bug fixes

This release includes updates to the True Append functionality and general improvements to the HIV-TRACE pipeline.

0.9.1

What's Changed

• Update setup.py by @stevenweaver in #107

Full Changelog: 0.8.0...0.9.1

0.8.0

What's Changed

• Create Dockerfile by @niemasd in #94
• Create devcontainer.json by @niemasd in #95
• Update README.md by @stevenweaver in #98
• Dockerfile -> RHEL 8 by @niemasd in #102
• Attempted fix for True Append code by @niemasd in #106
• true append initial commit by @stevenweaver in #105

Full Changelog: 0.7.1...0.8.0

0.7.1

What's Changed

• feat: only unpack resources if necessary by @FynnFreyer in #92
• fix: amend syntax error in except statement by @FynnFreyer in #90

New Contributors

• @FynnFreyer made their first contribution in #92

Full Changelog: 0.6.3...0.7.1

0.7.0

What's Changed

• master sync by @stevenweaver in #68
• Move to reporting singletons to hivnetworkcsv; run hivnetworkcsv in quiet mode by @stevenweaver in #71
• removing -o flag from hivnetworkcsv since it is no longer needed with… by @stevenweaver in #72

Full Changelog: 0.5.0...0.7.0

0.6.3

What's Changed

• master sync by @stevenweaver in #68
• Move to reporting singletons to hivnetworkcsv; run hivnetworkcsv in quiet mode by @stevenweaver in #71
• removing -o flag from hivnetworkcsv since it is no longer needed with… by @stevenweaver in #72

Full Changelog: 0.5.0...0.6.3

0.5.0

1.5.0 (#67)

* version bump

0.4.6

Adds new --do-not-store-intermediate flag, use to avoid exceptions when running hivtrace on the same dataset, in the same directory, at the same time.