polars-bio

What problem does it solve?

polars-bio provides a high-performance toolkit for genomic interval arithmetic and bioinformatics file I/O on Polars DataFrames, enabling fast overlap, nearest, merge, coverage, and related analyses with streaming and cloud-native capabilities to scale to large datasets.

Core Features & Use Cases

• Genomic interval operations: overlap, nearest, merge, cluster, coverage, complement, and subtract for BED/VCF/BAM/GFF data.
• Bioinformatics file I/O: read and write BED, VCF, BAM, CRAM, GFF/GTF, FASTA, and FASTQ with cloud storage and streaming support.
• SQL data processing: register files as SQL tables and query them with DataFusion SQL to combine with Polars pipelines.
• Pileup/depth: compute per-base or block depth from BAM/CRAM files with pb.depth.
• API styles: functional pb.* operations and method-chaining via LazyFrame.pb for fluent pipelines.
• Streaming/out-of-core: scan_* functions enable out-of-core processing for datasets larger than memory.
• Cross-cloud I/O: direct cloud URIs for S3/GCS/Azure read/write.

Quick Start

Overlap two interval datasets with pb.overlap and collect the results.