Fibertig

[mrvollger]

FiberTig Branch: PanGenome Support + Boundary Bug Fix

🎯 Overview

This PR introduces the first pangenome support to fibertools-rs while fixing a coordinate mapping bug (Issue #90). The changes add 3 new commands.

🐛 Bug Fix: Issue #90

Problem: Nucleosome/MSP coordinates at alignment block boundaries were incorrectly extended into subsequent blocks, causing artificial length inflation.

🚀 New Features: PanGenome Commands

1. pg-inject

Create mock BAM files from reference FASTA with perfectly aligned sequences while injecting annotation information from BED files.

3. pg-pansn

Add/strip panSN-spec prefixes from BAM contig names

• Full panSN specification compliance
• Bidirectional prefix management

2. pg-lift

Lift annotations through pangenome graphs from source to target coordinates

• Coordinate transformation across pangenome references
• Maintains annotation integrity during lifting
• Uses vg + pg-pansn + pg-lift under the hood.

📦 New Core Architecture

Major New Modules

• fibertig.rs (647 lines) - Core pangenome annotation framework
• bamannotations.rs (573 lines) - BED annotation handling & coordinate mapping
• panspec.rs (63 lines) - PanSN specification support

Enhanced Modules

• bamlift.rs - Improved coordinate lifting with better error handling
• bio_io.rs - Enhanced I/O capabilities (+114 lines)
• fiber.rs - Major cleanup and simplification (-218 lines)

Removed Legacy Code

• bamranges.rs (355 lines removed) - Replaced with more efficient implementations

Python (py-ft) Enhancements

• fiberplot - Standalone CLI tool for generating Altair HTML visualizations
• Updated dependencies and improved compatibility across the Python package