Polars

When to Use This Skill

Use this skill when:

• Performing genomic interval operations (overlap, nearest, merge, coverage, complement, subtract)
• Reading/writing bioinformatics file formats (BED, VCF, BAM, CRAM, GFF/GTF, FASTA, FASTQ)
• Processing large genomic datasets that don't fit in memory (streaming mode)
• Running SQL queries on genomic data files
• Migrating from bioframe to a faster alternative
• Computing read depth/pileup from BAM/CRAM files
• Working with Polars DataFrames containing genomic intervals

Basic Overlap Example

import polars as pl
import polars_bio as pb

## Create two interval DataFrames

df1 = pl.DataFrame({
    "chrom": ["chr1", "chr1", "chr1"],
    "start": [1, 5, 22],
    "end":   [6, 9, 30],
})

df2 = pl.DataFrame({
    "chrom": ["chr1", "chr1"],
    "start": [3, 25],
    "end":   [8, 28],
})