Bltools V2.2 May 2026

This command processes your Jinja templates and writes the raw SQL to the ./target/ directory without executing anything. It is useful for code reviews.

Solution: Ensure your rule file is saved with UTF-8 encoding and uses uppercase keywords as per RQL 2.0.

4.1 Adapter and Quality Trimming (bltrim) bltools v2.2

4.2 Streaming Conversion & Interleaving (blfastq2bam)

4.3 Duplicate marking (bldedup)

UMI-aware duplicate handling: optional UMI whitelist, hamming-distance tolerant grouping, and consensus calling.

4.4 BAM Cleanup (blbamclean)

4.5 Base Quality Recalibration (blrecal) This command processes your Jinja templates and writes

4.6 Variant Filtering (blfilter)

Vectorized evaluation per record; supports user-defined functions for allele-balance, strand-bias.

4.7 Statistics & Reporting (blstats)

pip install bltools==2.2.0

The flagship command. It executes all models (or selected ones) in dependency order. Vectorized evaluation per record

# Run all models
bltools run --target dev