Expand description
§genomicframe-core
High-performance, memory-efficient genomics I/O and interoperability layer written in Rust.
§Phase 1: Core Format Support
This crate provides efficient readers and writers for major bioinformatics formats:
- VCF/BCF (Variant Call Format)
- BAM/CRAM (Binary Alignment Map)
- FASTA/FASTQ (Sequence formats)
- GFF/GTF (Gene annotations)
§Architecture
- Zero-copy parsing where possible
- Memory-mapped I/O for large files
- Arrow-compatible columnar representations
- Lazy and eager iteration models
- Optional async I/O and cloud storage support
Modules§
- core
- Core types and traits for genomic data representation
- error
- Error types for genomicframe-core
- execution
- Execution engine that converts logical plans into filtered readers
- expression
- Expression system for GenomicFrame query language
- filtered_
reader - Filtered reader wrapper for applying filters during iteration
- filters
- Common filtering traits and combinators for all genomic formats
- formats
- Format-specific readers, writers, and utilities
- interval
- Genomic interval operations
- io
- I/O abstractions for local, async, and cloud storage
- parallel
- Parallel processing infrastructure for genomic data
- plan
- Logical query plan representation for GenomicFrame
- prelude
- Convenience module for glob imports
- schema
- Schema system for genomic data formats
- stats
- Shared statistics utilities for genomic data
- utils
- Utility functions and helpers