v0.2.0

[dialvarezs]

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[Copilot]

Pull request overview

This PR introduces v0.2.0 with significant enhancements to readfaker, including BAM format support, multi-base indel error modeling, and a dependency migration from needletail/bgzip to noodles for improved file I/O handling.

• Adds BAM file support for both input (model extraction) and output (read generation)
• Implements geometric distribution for multi-base insertions and deletions with configurable extension rates
• Migrates from needletail/bgzip to noodles library for unified FASTA/FASTQ/BAM handling

Reviewed changes

Copilot reviewed 10 out of 12 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
src/utils.rs	Added BAM support to load_models with automatic format detection based on file extension
src/models/error.rs	Added insertion/deletion extension rates with geometric distribution sampling for multi-base indels
src/main.rs	Integrated error model CLI parameters and added output format detection (BAM vs FASTQ)
src/io/mod.rs	Added BAM module and re-exported BAM reader/writer types
src/io/fastq.rs	Migrated from needletail to noodles, improved compression handling with configurable thread count
src/io/fasta.rs	Migrated from needletail to noodles for FASTA reading
src/io/bam.rs	New module implementing BAM file reading and writing with proper quality score encoding
src/generator.rs	Updated to work with noodles FASTQ record types
src/cli.rs	Added CLI parameters for error model configuration and compression threads
Cargo.toml	Replaced needletail/bgzip with noodles and flate2 dependencies
Cargo.lock	Updated dependency tree reflecting noodles migration
.gitignore	Added AI agent directories to gitignore

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